Contacts of the helix formed by residues 37 - 48 (chain A) in PDB entry 6FF8
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLY 3.3 1.4 - - - -
36A VAL* 1.4 79.5 - - - +
38A LYS* 1.3 66.3 + - - +
39A THR 3.2 2.9 - - - -
40A SER 3.2 0.2 + - - -
41A ILE* 2.9 31.9 + - - +
143A ASN* 3.6 11.2 - - - -
900A GTP 3.0 30.8 + - - -
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Residues in contact with LYS 38 (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 VAL* 3.7 26.2 - - + +
31A ILE 3.5 7.4 - - - +
32A GLY* 3.2 29.9 + - - +
33A GLU 3.0 19.8 + - - -
36A VAL* 3.9 11.1 - - + +
37A GLY* 1.3 76.2 - - - +
39A THR* 1.3 63.0 + - - +
41A ILE* 3.4 3.6 + - - +
42A ILE* 3.3 26.1 + - - +
81A ASP* 3.4 15.0 - - - +
82A ILE 2.9 29.2 - - - +
84A GLY 3.9 0.9 - - - +
105A VAL* 4.3 5.2 - - + -
900A GTP 2.6 52.0 + - - +
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Residues in contact with THR 39 (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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38A LYS* 1.3 76.1 - - - +
40A SER* 1.3 58.5 + - - +
42A ILE* 3.4 6.4 + - - +
43A LYS* 3.0 32.1 + - + +
55A ARG 5.4 3.8 - - - +
57A THR* 2.9 4.3 + - - +
61A ASP* 4.9 8.5 - - - +
81A ASP* 2.4 28.0 + - - +
900A GTP 2.9 12.5 + - - +
901A MG 2.2 30.6 - - - -
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Residues in contact with SER 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 GLY 3.8 1.3 - - - -
39A THR* 1.3 75.3 - - - +
41A ILE* 1.3 66.0 + - - +
43A LYS* 4.1 6.9 - - - +
44A ARG* 3.0 25.5 + - - +
49A LEU 4.5 2.2 - - - +
50A PHE* 4.3 10.9 - - - +
51A SER 4.6 3.7 + - - -
175A ALA* 3.4 11.7 - - - +
900A GTP 2.6 57.0 + - - -
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Residues in contact with ILE 41 (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 VAL* 5.5 5.2 - - + -
37A GLY 2.9 18.5 + - - +
38A LYS* 3.8 4.3 - - - +
40A SER* 1.3 74.8 - - - +
42A ILE* 1.3 63.4 + - + +
44A ARG* 3.8 1.2 - - - +
45A TYR* 3.0 30.1 + - + +
103A PHE* 5.9 4.9 - - + -
105A VAL* 3.8 27.4 - - + -
141A LEU* 4.2 17.9 - - + -
143A ASN* 3.4 39.0 - - + +
173A THR* 4.1 6.3 - - - +
175A ALA* 3.9 10.3 - - + -
181A ILE* 4.1 25.6 - - + +
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Residues in contact with ILE 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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30A VAL* 3.7 29.8 - - + -
38A LYS 3.3 16.0 + - - +
39A THR 3.6 5.8 - - - +
40A SER 3.2 0.2 - - - -
41A ILE* 1.3 80.8 - - + +
43A LYS* 1.3 57.9 + - - +
45A TYR* 3.4 4.0 + - - -
46A VAL* 2.8 36.7 + - + +
47A HIS* 6.4 0.4 - - + -
62A PHE 5.6 0.4 - - - -
63A ALA* 3.5 31.9 - - + -
79A LEU* 4.1 21.8 - - + +
81A ASP* 3.5 36.1 - - + +
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Residues in contact with LYS 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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39A THR* 3.0 23.0 + - + +
40A SER* 3.5 7.4 + - - +
42A ILE* 1.3 76.9 - - - +
44A ARG* 1.3 57.7 + - - +
47A HIS* 2.8 45.6 + - + +
48A GLN 3.1 5.2 + - - -
49A LEU* 3.5 44.9 + - + +
50A PHE* 4.2 6.0 - - - +
51A SER* 3.8 24.3 - - - +
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Residues in contact with ARG 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 SER 3.0 17.7 + - - +
41A ILE 3.8 3.4 - - - +
43A LYS* 1.3 76.7 - - - +
45A TYR* 1.3 60.1 + - - +
48A GLN* 2.9 78.9 + - - +
49A LEU* 3.3 14.7 + - - +
50A PHE* 3.5 18.6 - - - +
175A ALA* 2.9 25.5 + - + +
176A LYS 2.8 27.4 + - - -
177A ASP 5.0 0.2 - - - -
178A ASN* 3.4 33.9 - - - +
181A ILE* 4.1 11.7 - - + -
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Residues in contact with TYR 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 ILE* 3.0 19.5 + - + +
42A ILE* 3.9 4.5 - - - +
44A ARG* 1.3 79.5 - - - +
46A VAL* 1.3 65.4 + - + +
48A GLN* 4.5 6.0 + - - +
65A LYS* 2.9 61.7 + - + +
67A LEU* 3.7 29.5 - - + +
77A LEU* 4.3 10.8 - - + +
79A LEU* 4.7 9.2 - - + -
103A PHE* 5.9 4.0 - + - -
181A ILE* 3.6 20.9 - - + -
182A GLU* 3.3 37.9 + - - +
185A ALA* 3.1 33.3 - - + +
186A ARG* 4.9 0.7 + - - +
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Residues in contact with VAL 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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42A ILE* 2.8 28.3 + - + +
45A TYR* 1.3 77.6 - - + +
47A HIS* 1.3 87.9 + - + +
48A GLN* 3.6 0.8 - - - +
63A ALA* 4.2 9.6 - - + -
64A LEU 3.5 20.2 - - - +
65A LYS* 4.1 21.5 + - + +
79A LEU* 4.0 26.5 - - + -
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Residues in contact with HIS 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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42A ILE* 6.4 0.2 - - + -
43A LYS* 2.8 30.3 + - + +
46A VAL* 1.3 100.2 + - + +
48A GLN* 1.3 71.8 + - - +
49A LEU* 3.6 26.1 - - + +
63A ALA* 5.5 4.4 - - + +
55B ARG* 6.3 0.4 - - - -
58B ILE* 6.5 0.4 - - + -
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Residues in contact with GLN 48 (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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44A ARG* 2.9 68.6 + - - +
45A TYR* 4.5 3.7 + - - +
46A VAL 3.6 1.0 - - - -
47A HIS* 1.3 79.7 - - - +
49A LEU* 1.3 65.4 + - - +
178A ASN* 3.5 26.7 + - - +
182A GLU* 3.9 17.0 + - - -
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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
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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