Contacts of the helix formed by residues 12 - 34 (chain B) in PDB entry 4ZGM
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 PHE 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLY* 3.8 23.1 - - - -
11B THR* 1.3 82.1 - - - +
13B THR* 1.3 62.4 + - + +
14B SER* 3.1 14.6 - - - +
15B ASP* 2.8 40.0 + - - +
16B VAL* 3.3 6.8 + - - +
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 1.3 75.2 - - + +
14B SER* 1.3 62.3 + - - +
16B VAL* 3.2 11.6 + - - +
17B SER* 3.0 27.3 + - - -
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.0 12.0 - - - +
13B THR* 1.3 82.8 - - - +
15B ASP* 1.3 64.9 + - - +
17B SER* 3.0 9.0 + - - -
18B SER* 3.0 33.9 + - - -
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY 4.2 1.9 - - - +
11B THR* 3.5 23.0 - - + +
12B PHE* 2.8 42.0 + - - +
14B SER* 1.3 81.3 + - - +
16B VAL* 1.3 56.8 + - - +
18B SER* 3.9 4.5 - - - -
19B TYR* 3.0 28.1 + - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B THR* 4.6 11.7 - - + -
12B PHE 4.0 9.6 - - - +
13B THR* 3.2 13.1 + - - +
15B ASP* 1.3 76.2 - - - +
17B SER* 1.3 61.0 + - - +
19B TYR* 3.3 10.1 + - + +
20B LEU* 2.9 42.9 + - + +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR* 3.0 10.6 + - - -
14B SER* 3.0 20.1 + - - -
16B VAL* 1.3 77.4 - - - +
18B SER* 1.3 65.5 + - - +
20B LEU* 3.3 11.0 + - - +
21B GLU* 3.1 29.8 + - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 3.9 18.7 - - - +
14B SER* 3.0 17.1 + - - -
15B ASP* 4.0 5.2 - - - -
17B SER* 1.3 76.9 + - - +
19B TYR* 1.3 65.8 + - - +
21B GLU* 3.3 11.1 + - - +
22B GLY* 2.9 22.0 + - - -
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP 3.0 19.0 + - - +
16B VAL* 3.3 11.2 + - + +
18B SER* 1.3 76.4 - - - +
20B LEU* 1.3 68.6 + - + +
22B GLY* 3.3 1.3 + - - -
23B GLN* 2.9 70.7 + - + +
26B LYS* 5.9 1.8 - - - -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 2.9 31.7 + - + +
17B SER* 3.6 10.3 - - - +
18B SER 3.2 0.2 - - - -
19B TYR* 1.3 87.2 - - + +
21B GLU* 1.3 62.1 + - + +
23B GLN* 3.2 6.9 + - + +
24B ALA* 3.2 18.5 + - - +
101B 32M 3.6 37.0 - - - +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 4.5 14.4 - - + +
30A VAL 4.4 6.9 - - - +
31A SER* 5.6 6.9 - - - -
32A LEU 4.6 4.5 + - - -
17B SER* 3.1 17.0 + - - +
18B SER* 3.7 9.9 + - - +
20B LEU* 1.3 72.5 - - + +
22B GLY* 1.3 66.8 + - - +
24B ALA* 3.2 20.7 + - - +
25B ALA* 3.5 4.0 + - - +
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 4.4 10.9 - - - +
30A VAL 4.4 11.4 - - - -
18B SER 2.9 14.9 + - - -
19B TYR* 3.6 4.0 - - - -
21B GLU* 1.3 76.6 - - - +
23B GLN* 1.3 61.0 + - - +
25B ALA* 3.3 5.9 + - - +
26B LYS* 3.1 38.2 + - - +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 2.9 62.8 + - + +
20B LEU* 3.6 8.3 - - + +
21B GLU 3.1 0.4 - - - -
22B GLY* 1.3 74.7 - - - +
24B ALA* 1.3 60.6 + - - +
26B LYS* 3.4 34.8 - - - +
27B GLU* 2.8 52.4 + - + +
101B 32M 4.0 14.1 - - - -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.6 26.9 - - + +
20B LEU 3.2 11.3 + - - +
21B GLU* 3.2 13.0 + - - +
23B GLN* 1.3 76.7 - - - +
25B ALA* 1.3 62.2 + - - +
27B GLU 3.4 0.2 + - - -
28B PHE 3.1 16.5 + - - -
101B 32M 3.3 37.8 - - - +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL 3.9 17.7 - - - +
31A SER 4.0 6.5 - - - +
32A LEU* 4.0 13.5 - - - +
35A THR* 3.8 22.9 - - - +
90A PRO* 4.1 11.7 - - + -
21B GLU 3.5 2.4 + - - +
22B GLY 3.3 8.3 + - - +
23B GLN 3.3 0.4 - - - -
24B ALA* 1.3 80.1 - - - +
26B LYS* 1.3 61.8 + - - +
28B PHE* 3.1 5.9 + - - +
29B ILE* 3.0 26.7 + - - +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PRO* 5.2 6.3 - - + +
91A TRP* 4.0 19.7 - - + -
128A GLU* 2.8 43.5 + - - +
19B TYR* 5.9 1.8 - - - -
22B GLY* 3.1 21.7 + - - +
23B GLN* 3.4 35.2 - - - +
25B ALA* 1.3 76.5 - - + +
27B GLU* 1.3 58.0 + - - +
29B ILE* 3.3 10.5 + - - +
30B ALA* 3.0 26.5 + - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 2.8 40.8 + - + +
24B ALA 3.8 3.8 - - - +
26B LYS* 1.3 69.9 - - - +
28B PHE* 1.3 66.0 + - - +
30B ALA* 3.3 12.4 + - - +
31B TRP* 2.9 24.4 + - - +
34B ARG* 4.7 7.4 + - - -
101B 32M 3.8 41.6 - - - +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.5 21.8 - - + -
35A THR* 3.9 22.0 - - + -
36A VAL* 3.9 28.0 - - + -
39A TRP* 4.0 30.7 - + + -
24B ALA 3.1 4.6 + - - +
25B ALA 3.1 7.7 + - - +
27B GLU* 1.3 78.2 - - - +
29B ILE* 1.3 66.6 + - + +
31B TRP* 3.1 36.8 + + - +
32B LEU* 2.9 50.9 + - + +
101B 32M 3.9 28.9 + - + +
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.9 21.1 - - + -
69A TYR* 4.6 5.4 - - + -
88A TYR* 3.6 30.1 - - + -
89A LEU* 3.8 21.5 - - + -
90A PRO* 3.9 18.6 - - + -
91A TRP* 4.1 17.3 - - + -
25B ALA 3.0 13.3 + - - +
26B LYS 3.6 6.7 - - - +
28B PHE* 1.3 75.7 - - + +
30B ALA* 1.3 64.2 + - - +
32B LEU* 3.0 11.9 + - + +
33B VAL* 2.9 33.2 + - + +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS 3.0 13.8 + - - +
27B GLU* 3.6 16.4 - - - +
28B PHE 3.3 0.2 - - - -
29B ILE* 1.3 77.8 - - - +
31B TRP* 1.3 58.0 + - - +
33B VAL* 3.3 9.4 + - - +
34B ARG* 3.0 46.5 + - - +
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Residues in contact with TRP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLU 2.9 13.9 + - - +
28B PHE* 3.1 42.4 + + - +
30B ALA* 1.3 74.3 - - - +
32B LEU* 1.3 63.7 + - + +
34B ARG* 3.3 32.8 + - + +
35B GLY 3.2 4.7 + - - -
36B ARG* 2.8 79.7 + - + -
37B GLY* 2.9 27.6 + - - -
101B 32M 3.8 39.7 - - + -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TRP* 3.4 42.8 - - + +
67A ASP 4.3 1.4 - - - +
68A GLU* 3.6 19.4 - - - +
69A TYR* 4.1 10.3 - - + +
88A TYR* 3.7 19.5 - - + +
121A ARG* 5.1 0.3 + - - -
28B PHE* 2.9 44.2 + - + +
29B ILE* 3.0 11.4 + - + +
31B TRP* 1.3 76.4 - - + +
33B VAL* 1.3 58.5 + - - +
35B GLY* 2.8 20.1 + - - -
36B ARG* 3.7 32.9 + - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.6 31.9 - - + -
121A ARG* 2.9 38.7 + - - +
123A LEU* 3.9 17.5 - - + -
29B ILE* 2.9 23.7 + - + +
30B ALA* 3.3 11.6 + - - +
32B LEU* 1.3 75.4 - - - +
34B ARG* 1.3 61.8 + - + +
35B GLY* 3.3 1.0 + - - -
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Residues in contact with ARG 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 4.7 7.3 + - - -
30B ALA* 3.0 36.1 + - - +
31B TRP* 3.5 44.1 - - + +
32B LEU 3.2 0.4 - - - -
33B VAL* 1.3 77.1 - - + +
35B GLY* 1.3 58.3 + - - +
36B ARG 4.8 0.9 - - - +
37B GLY* 4.9 2.9 + - - +
101B 32M 5.4 3.4 - - - -
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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