Contacts of the helix formed by residues 32 - 47 (chain A) in PDB entry 1NGS
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 GLY 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS 3.6 1.2 - - - -
31A PRO* 1.3 75.6 - - - +
33A ALA* 1.3 63.6 + - - +
35A LEU* 3.2 2.9 + - - +
36A GLY* 3.2 11.8 + - - -
250A ILE* 3.8 10.7 - - - +
251A GLY* 3.1 31.9 + - - -
262A VAL* 2.9 26.3 + - - -
263A HIS 4.2 1.9 + - - -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS* 5.3 0.6 - - - +
32A GLY* 1.3 68.3 - - - +
34A PRO* 1.3 68.2 - - + +
36A GLY* 3.0 1.8 + - - +
37A MET* 2.7 39.9 + - + +
67A ASN* 4.7 5.8 - - - +
69A HIS* 4.5 5.3 - - + +
70A ALA* 3.9 15.5 - - + -
185A ASP* 3.9 19.3 - - - +
187A ASN* 5.2 0.4 - - - +
250A ILE* 4.2 7.4 - - - +
263A HIS 5.4 0.8 + - - -
682A TPP 3.8 21.8 + - - +
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Residues in contact with PRO 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 5.4 0.2 - - - +
16A ARG* 4.8 1.9 - - - +
19A ALA* 4.1 21.9 - - + +
30A HIS* 3.0 28.3 - - + +
31A PRO* 3.3 12.3 - - + +
33A ALA* 1.3 93.9 - - + +
35A LEU* 1.3 61.0 + - + +
37A MET 3.9 0.3 - - - -
38A ALA* 3.2 26.7 + - - +
70A ALA* 3.6 20.2 - - + +
72A ALA* 4.7 6.5 - - + -
73A LEU* 4.0 30.8 - - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 2.8 65.4 + - + +
19A ALA* 6.0 0.4 - - + -
20A VAL* 3.5 32.3 - - + -
31A PRO* 3.1 21.3 + - + +
32A GLY 3.2 6.9 + - - +
33A ALA 3.1 0.6 - - - -
34A PRO* 1.3 79.5 - - + +
36A GLY* 1.3 58.3 + - - +
38A ALA 4.1 1.2 + - - -
251A GLY* 3.6 31.6 - - - +
252A TYR* 3.9 12.0 - - - +
254A SER* 4.6 1.6 - - - -
267A LEU* 4.1 16.2 - - + -
275A LEU* 4.5 10.3 - - + -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 4.7 1.0 + - - -
32A GLY 3.2 6.1 + - - -
33A ALA* 3.0 6.4 + - - -
35A LEU* 1.3 79.2 - - - +
37A MET* 1.3 63.8 + - - +
38A ALA 3.4 0.6 + - - -
39A PRO* 3.9 8.8 - - - +
40A ALA 5.3 0.2 + - - -
185A ASP* 5.3 0.7 - - - -
220A GLY 4.2 3.5 - - - +
221A ASN* 4.8 2.1 - - - +
246A MET* 4.8 0.7 - - - +
248A THR* 3.3 30.6 - - - +
249A THR 3.9 20.1 + - - -
250A ILE* 5.3 1.1 - - - -
252A TYR* 4.6 3.4 - - - -
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Residues in contact with MET 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 2.7 19.0 + - + +
34A PRO 3.9 0.4 - - - -
36A GLY* 1.3 74.9 - - - +
38A ALA* 1.3 63.1 + - - +
39A PRO 3.4 1.8 - - - -
40A ALA* 3.2 9.9 + - + +
41A ALA* 3.0 21.3 + - - +
65A LEU* 4.3 5.8 - - + -
67A ASN* 3.0 31.2 - - - +
70A ALA* 4.7 6.7 - - + -
73A LEU* 3.9 15.0 - - + -
154A PHE* 3.3 38.9 - - + -
155A LEU 5.1 0.4 - - - +
183A ILE* 5.3 2.0 - - - +
185A ASP* 3.5 43.7 - - - +
246A MET* 4.6 10.5 - - + -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 4.2 6.7 - - - +
15A ILE* 4.0 19.3 - - + +
16A ARG* 3.4 31.6 - - + -
34A PRO 3.2 14.1 + - - +
36A GLY 3.4 0.2 - - - -
37A MET* 1.3 76.3 - - - +
39A PRO* 1.3 71.3 - - + +
41A ALA* 3.2 2.4 + - - +
42A HIS* 3.0 23.4 + - - +
73A LEU* 3.9 9.4 - - - -
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Residues in contact with PRO 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.9 13.5 - - + -
16A ARG* 3.7 24.9 - - - +
36A GLY 3.9 7.6 - - - +
37A MET 3.7 2.2 - - - -
38A ALA* 1.3 93.6 - - + +
40A ALA* 1.3 61.1 + - - +
42A HIS* 3.4 1.7 + - - +
43A VAL* 3.0 28.1 + - - +
220A GLY 3.6 16.6 - - - +
221A ASN 3.7 23.6 - - - +
222A GLU* 5.2 1.8 - - - +
224A LEU* 3.7 20.8 - - + +
227A ILE* 4.1 6.3 - - + -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A MET* 3.2 10.0 + - - +
38A ALA 3.2 0.4 - - - -
39A PRO* 1.3 80.6 - - - +
41A ALA* 1.3 58.3 + - - +
43A VAL* 3.4 1.6 + - - +
44A LEU* 2.8 32.6 + - - +
154A PHE* 3.9 17.3 - - + -
183A ILE* 4.7 4.6 - - + +
220A GLY 5.0 0.6 + - - -
227A ILE* 3.9 17.9 - - + +
231A ILE* 5.1 0.2 - - - +
246A MET* 3.8 35.4 - - + -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET 3.0 11.7 + - - +
38A ALA 3.2 8.0 + - - +
40A ALA* 1.3 73.2 - - - +
42A HIS* 1.3 67.4 - - - +
44A LEU* 3.2 0.4 + - - -
45A TRP* 2.8 36.9 + - + +
63A PHE* 6.2 0.2 - - + -
73A LEU* 3.7 22.7 - - + -
77A MET* 4.1 19.7 - - + -
154A PHE* 3.8 17.8 - - + -
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Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 5.1 3.8 - + - -
8A ASP* 3.0 42.9 + - + -
11A ALA* 3.4 23.4 - - + +
12A VAL* 3.7 22.2 - - + -
15A ILE* 4.1 5.5 - - + +
38A ALA 3.0 6.1 + - - +
39A PRO 3.6 6.7 - - - +
41A ALA* 1.3 80.9 - - - +
43A VAL* 1.3 69.8 + - + +
45A TRP* 4.2 0.5 - - - +
46A SER* 2.6 42.8 + - - -
77A MET* 4.4 4.9 - - - +
224A LEU* 4.8 3.4 - - + -
296A HIS* 3.9 10.5 - + - -
297A TYR* 2.5 38.9 + + - +
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Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 4.3 14.5 - - + -
39A PRO 3.0 18.0 + - - +
40A ALA 3.8 3.1 - - - +
42A HIS* 1.3 81.6 - - + +
44A LEU* 1.3 63.0 + - - +
46A SER* 3.7 5.1 - - - -
47A GLN* 3.5 20.5 + - + +
224A LEU* 3.2 37.2 - - + +
227A ILE* 4.2 13.0 - - + -
228A ALA* 3.8 37.5 - - + +
231A ILE* 4.3 5.8 - - + +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 2.8 22.4 + - - +
41A ALA* 3.8 2.5 - - - +
43A VAL* 1.3 71.9 - - - +
45A TRP* 1.3 70.2 + - + +
47A GLN* 2.9 41.4 + - - +
48A MET* 3.1 8.4 + - - +
63A PHE* 3.8 24.0 - - + -
152A TYR* 3.7 39.7 - - + -
153A VAL 5.6 0.4 - - - +
154A PHE* 3.6 28.0 - - + -
183A ILE* 4.4 6.5 - - + -
231A ILE* 4.1 17.2 - - + +
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Residues in contact with TRP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 2.8 34.1 + - + +
42A HIS 4.2 0.7 - - - +
44A LEU* 1.3 83.5 - - + +
46A SER* 1.3 63.4 + - - +
47A GLN 3.1 1.3 + - - -
48A MET* 3.2 18.3 + - + +
50A MET* 3.3 38.9 - - + +
63A PHE* 3.8 47.8 - + + -
74A LEU* 4.0 16.4 - - + -
77A MET* 3.7 42.6 - - + +
78A LEU* 4.3 10.3 - - + -
81A THR* 3.7 30.3 - - + -
83A TYR* 4.2 12.3 - + - -
110A GLY 5.4 2.9 - - - -
297A TYR* 5.7 0.2 - - + -
301A ILE* 3.5 13.0 - - + +
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE* 6.0 4.5 - - - -
8A ASP* 6.0 0.4 - - - -
42A HIS* 2.6 43.2 + - - -
43A VAL* 3.7 7.4 - - - -
44A LEU 3.2 0.2 - - - -
45A TRP* 1.3 76.8 - - - +
47A GLN* 1.3 58.7 + - - +
48A MET 4.8 1.6 - - - +
296A HIS* 5.2 1.5 - - - -
297A TYR* 4.1 7.8 - - - -
300A THR* 3.9 31.2 - - - +
301A ILE* 3.8 12.5 - - - +
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 3.5 12.8 - - + +
44A LEU* 2.9 40.8 + - - +
46A SER* 1.3 81.0 - - - +
48A MET* 1.3 59.0 + - - +
49A ARG* 4.0 1.2 + - - +
61A ASP* 4.3 2.8 - - - +
152A TYR* 2.9 23.0 + - - -
231A ILE* 3.9 14.7 - - + +
235A LYS* 3.0 30.2 + - - +
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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
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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