Contacts of the helix formed by residues 27 - 47 (chain K) in PDB entry 2GTL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 27 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I SER* 3.3 29.0 - - - +
27I PHE* 3.8 27.8 - - + +
29I ASP* 3.9 12.9 - - - +
30I ARG* 3.6 28.4 + - - +
13J LYS* 3.1 26.4 + - - +
80J ASP* 4.4 6.0 - - - +
25K ASP* 3.0 8.6 + - - +
26K THR* 1.3 78.9 + - - +
28K SER* 1.3 63.6 + - - +
29K SER* 3.2 10.0 + - - -
30K LYS* 3.3 18.2 + - + +
31K ILE* 3.4 13.3 + - - +
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Residues in contact with SER 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LYS* 5.6 0.3 - - - -
73J ASP* 5.4 1.2 + - - -
77J SER* 4.4 13.7 - - - -
23K TRP* 4.6 18.4 - - - -
25K ASP 3.6 8.4 + - - -
26K THR 2.9 9.2 + - - -
27K GLU* 1.3 75.3 - - - +
29K SER* 1.3 58.9 + - - +
31K ILE* 3.0 9.5 + - - +
32K LYS* 2.7 59.4 + - - +
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Residues in contact with SER 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LYS* 3.5 12.8 + - - +
77J SER* 3.2 31.1 + - - -
78J THR* 4.5 5.6 - - - -
81J GLN* 3.2 22.1 + - - -
26K THR 4.8 0.2 + - - -
27K GLU* 3.7 5.7 + - - -
28K SER* 1.3 80.3 + - - +
30K LYS* 1.3 71.2 + - - +
32K LYS* 4.6 1.3 - - - -
33K ILE* 2.9 35.2 + - - +
72K LEU* 4.5 11.0 - - - -
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Residues in contact with LYS 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PHE* 3.5 34.7 - - + -
29I ASP* 3.1 35.8 + - - +
80J ASP* 5.4 0.9 + - - -
81J GLN* 3.8 30.0 + - - +
27K GLU* 3.3 17.6 + - + +
29K SER* 1.3 83.4 + - - +
31K ILE* 1.3 57.1 + - - +
33K ILE* 4.0 6.9 - - + +
34K GLY* 3.1 23.9 + - - -
85L ASP* 4.8 6.1 - - + +
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Residues in contact with ILE 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PHE* 3.7 25.4 - - + -
22K LEU* 3.8 20.2 - - + +
23K TRP* 3.4 24.7 - - + -
25K ASP* 3.6 24.7 - - - +
27K GLU 3.4 6.7 + - - +
28K SER* 3.0 8.7 + - - +
30K LYS* 1.3 72.5 - - - +
32K LYS* 1.3 71.2 + - - +
33K ILE 2.8 2.2 + - - -
34K GLY* 3.0 2.5 + - - -
35K PHE* 2.8 29.1 + - + +
15L LEU* 3.8 38.4 - - + -
19L LEU* 5.1 2.5 - - + -
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Residues in contact with LYS 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J ASP* 3.1 19.8 + - - -
77J SER* 5.8 1.0 + - - -
23K TRP* 3.8 33.1 - - + +
28K SER* 2.7 38.8 + - - +
29K SER* 5.1 0.9 - - - +
31K ILE* 1.3 74.1 - - - +
33K ILE* 1.3 53.6 + - - +
35K PHE* 4.6 2.0 - - - -
36K GLY* 2.7 34.0 + - - -
71K ALA 4.6 0.3 - - - +
72K LEU* 3.6 22.4 - - + -
75K LEU* 3.5 35.2 - - + +
76K ASN* 3.0 29.3 + - + +
79K ASP* 4.3 10.8 + - - -
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Residues in contact with ILE 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J THR* 5.4 0.2 - - + -
81J GLN* 4.1 22.9 - - - +
84J THR* 4.9 3.6 - - + -
29K SER* 2.9 27.1 + - - +
30K LYS* 4.0 7.2 - - + +
31K ILE 2.8 2.8 + - - -
32K LYS* 1.3 69.6 - - - +
34K GLY* 1.3 61.9 + - - +
36K GLY 3.5 0.2 - - - -
37K ARG* 2.5 49.5 + - + +
68K SER* 3.9 39.0 - - - +
71K ALA* 4.0 9.2 - - + +
72K LEU* 3.4 31.6 - - + -
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Residues in contact with GLY 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K LYS 3.1 10.1 + - - -
31K ILE* 3.0 7.6 + - - -
33K ILE* 1.3 78.3 - - - +
35K PHE* 1.3 56.3 + - - +
37K ARG* 3.4 13.9 - - - +
38K LEU* 2.9 30.5 + - - +
11L VAL* 4.4 19.7 - - - +
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Residues in contact with PHE 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K TRP* 4.8 8.3 - + - -
22K LEU* 5.4 7.0 - - + -
23K TRP* 5.8 1.1 - + - -
31K ILE* 2.8 28.6 + - + +
32K LYS* 3.9 3.8 - - - +
34K GLY* 1.3 71.4 - - - +
36K GLY* 1.3 56.5 + - - +
38K LEU* 3.2 8.0 + - + +
39K LEU* 2.8 65.6 + - + +
75K LEU* 3.8 16.6 - - + -
120K LEU* 4.4 1.8 - - + -
123K GLY* 4.3 9.2 - - - -
124K LEU* 3.8 40.2 - - + -
127K VAL* 3.9 32.3 - - + -
11L VAL* 5.0 2.8 - - - +
12L THR* 4.5 14.1 - - + -
15L LEU* 5.4 5.1 - - + +
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Residues in contact with GLY 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K LYS 2.7 22.2 + - - -
35K PHE* 1.3 73.4 - - - +
37K ARG* 1.3 62.2 + - - +
39K LEU* 3.3 6.4 + - - +
40K LEU* 3.0 30.9 + - - +
71K ALA* 4.3 10.3 - - - -
74K ILE* 5.4 3.6 - - - -
75K LEU* 4.1 21.5 - - - -
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Residues in contact with ARG 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K ILE* 2.5 39.0 + - + +
34K GLY* 3.4 11.3 - - - +
36K GLY* 1.3 73.4 - - - +
38K LEU* 1.3 68.5 + - - +
40K LEU* 3.8 1.9 - - - +
41K THR* 2.9 29.1 + - - +
62K ALA* 3.5 41.1 + - + +
63K GLU* 3.3 37.6 + - - +
67K PHE* 4.2 15.4 - - + -
68K SER* 4.9 0.6 + - - -
71K ALA* 4.0 5.9 - - + +
11L VAL* 5.8 6.9 - - - +
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Residues in contact with LEU 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K GLY 2.9 17.4 + - - +
35K PHE* 3.5 7.4 - - + +
37K ARG* 1.3 82.4 - - - +
39K LEU* 1.3 81.5 + - + +
41K THR* 3.1 6.7 + - - -
42K LYS* 2.8 33.4 + - + +
119K ILE* 5.5 0.7 - - + -
123K GLY* 6.1 3.1 - - - -
126K GLN* 5.6 1.3 - - - +
10L LEU* 5.3 8.5 - - + -
11L VAL* 4.2 21.8 - - + +
12L THR* 3.5 32.1 - - + +
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Residues in contact with LEU 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K PHE* 2.8 60.0 + - + +
36K GLY* 3.6 5.8 - - - +
38K LEU* 1.3 86.0 - - + +
40K LEU* 1.3 61.9 + - + +
42K LYS* 3.7 4.5 + - - +
43K LEU* 3.3 17.5 + - - +
74K ILE* 6.0 1.3 - - + -
75K LEU* 4.3 12.1 - - + -
78K LEU* 5.7 0.4 - - + -
116K PHE* 4.1 22.2 - - + -
119K ILE* 4.1 28.1 - - + +
120K LEU* 3.4 34.3 - - + +
123K GLY* 5.1 3.1 - - - -
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Residues in contact with LEU 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K GLY 3.0 21.1 + - - +
37K ARG 3.8 2.5 - - - +
39K LEU* 1.3 72.0 - - - +
41K THR* 1.3 67.4 + - - +
43K LEU* 2.8 18.1 + - + +
44K ALA* 3.0 14.1 + - - +
54K PHE* 3.6 29.8 - - + -
59K ILE* 5.0 3.5 - - + +
67K PHE* 3.8 20.6 - - + -
70K HIS* 3.4 36.8 - - + +
71K ALA* 4.7 2.5 - - - -
74K ILE* 3.7 33.2 - - + -
116K PHE* 4.0 14.6 - - + -
160K HEM 5.8 1.3 - - + -
161K CMO 4.2 0.4 - - - +
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Residues in contact with THR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K ARG* 2.9 27.8 + - - +
38K LEU* 3.4 11.1 - - - -
40K LEU* 1.3 75.3 - - - +
42K LYS* 1.3 55.7 + - - +
43K LEU 2.8 10.2 + - - -
44K ALA* 2.8 19.3 + - + +
45K LYS* 2.9 15.9 + - + +
59K ILE* 5.4 5.5 - - - +
62K ALA* 4.8 7.8 - - - +
67K PHE* 4.9 4.8 - - - -
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Residues in contact with LYS 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K LEU* 2.8 29.0 + - + +
39K LEU 4.0 3.8 - - - +
41K THR* 1.3 74.6 - - - +
43K LEU* 1.3 61.1 + - - +
45K LYS* 3.8 18.2 - - + +
46K ASP* 3.6 39.5 + - - -
119K ILE* 3.6 31.9 - - + +
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Residues in contact with LEU 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K LEU 3.3 11.7 + - - +
40K LEU* 2.8 13.5 + - + +
41K THR 2.8 0.2 + - - -
42K LYS* 1.3 75.1 - - - +
44K ALA* 1.3 59.0 + - - +
45K LYS 3.0 4.3 + - - -
46K ASP* 3.1 4.0 + - - +
47K ILE* 2.9 30.2 + - + +
50K VAL* 4.2 24.0 - - + -
54K PHE* 4.7 6.5 - - + -
112K HIS* 4.1 19.3 - - + +
115K LYS* 4.1 10.1 - - + -
116K PHE* 4.1 22.2 - - + +
119K ILE* 3.6 20.2 - - + -
160K HEM 3.9 30.7 - - + -
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Residues in contact with ALA 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K LEU 3.0 8.9 + - - +
41K THR* 2.8 10.4 + - - +
43K LEU* 1.3 75.9 - - - +
45K LYS* 1.3 62.4 + - - +
47K ILE 3.5 10.1 - - - -
48K PRO* 3.3 22.9 - - - +
50K VAL* 4.2 5.6 - - + +
51K ASN* 3.5 35.8 + - - +
59K ILE* 4.2 15.0 - - + -
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Residues in contact with LYS 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K THR* 2.9 18.3 + - + +
42K LYS* 3.6 24.7 - - + +
44K ALA* 1.3 80.3 - - - +
46K ASP* 1.3 70.3 + - - +
48K PRO* 4.7 3.6 - - - +
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Residues in contact with ASP 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K LYS* 3.6 32.7 + - - +
43K LEU 3.1 6.7 + - - +
45K LYS* 1.3 88.9 - - - +
47K ILE* 1.3 67.9 + - + +
48K PRO* 4.1 4.5 - - - +
115K LYS* 3.0 38.1 - - + +
119K ILE* 4.9 2.3 - - - +
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Residues in contact with ILE 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K LEU* 2.9 11.2 + - + +
44K ALA* 3.4 7.7 - - - +
46K ASP* 1.3 88.8 - - + +
48K PRO* 1.3 61.7 - - + +
49K GLU* 3.4 32.3 - - + +
50K VAL* 3.0 29.7 - - + +
111K ALA* 4.4 11.7 - - + +
112K HIS* 3.7 24.7 - - + +
115K LYS* 4.1 27.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il