Contacts of the strand formed by residues 55 - 62 (chain A) in PDB entry 2G98
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 TYR 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A MET* 3.4 5.5 - - - +
44A LEU* 2.8 47.7 + - + +
45A TYR 5.6 0.4 - - - -
46A GLU* 5.0 7.4 - - + -
53A LEU* 3.6 36.2 - - + +
54A GLN* 1.3 87.4 - - - +
56A PHE* 1.3 59.5 + - - +
57A LEU* 3.2 10.4 - - + +
68A TRP* 3.5 46.4 - + + +
69A MET* 3.2 19.5 - - + -
70A GLY* 3.5 11.2 - - - -
71A LEU* 3.5 31.0 + - + +
74A SER 5.6 3.8 - - - -
75A VAL* 6.1 1.3 - - + -
142A GLN* 3.7 9.4 - - - +
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Residues in contact with PHE 56 (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 CYS* 3.9 20.9 - - + -
42A TRP 3.5 9.9 - - - -
43A MET* 3.8 8.0 - - - +
55A TYR* 1.3 68.3 - - - +
57A LEU* 1.3 78.3 + - - +
58A ARG* 4.4 13.7 - - + -
62A TYR* 4.7 2.3 + - - -
68A TRP* 4.6 9.7 - - - +
81A ILE* 3.6 25.6 - - + -
131A VAL* 3.8 14.8 - - + -
133A TYR* 4.2 15.3 - - - +
142A GLN* 2.9 22.8 + - - +
167A ARG* 4.2 21.5 - - + -
168A ARG 5.4 0.4 - - - -
169A VAL* 3.8 28.5 - - + -
170A ILE 5.3 1.3 - - - -
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Residues in contact with LEU 57 (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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3A ILE* 4.4 3.8 - - + -
35A ALA* 4.0 10.1 - - + -
37A VAL* 4.1 13.7 - - + -
41A CYS* 3.6 2.3 - - - -
42A TRP* 2.9 40.9 + - + +
44A LEU* 3.8 33.0 - - + -
55A TYR* 3.2 22.7 - - + +
56A PHE* 1.3 85.1 - - - +
58A ARG* 1.3 60.7 + - - +
62A TYR* 3.5 39.0 - - + +
68A TRP* 3.8 26.2 - - + -
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Residues in contact with ARG 58 (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 VAL* 3.3 15.3 - - - +
40A GLY 4.2 6.5 - - - -
41A CYS* 4.6 9.2 - - - +
56A PHE* 4.4 19.3 - - + -
57A LEU* 1.3 74.8 - - - +
59A ARG* 1.3 69.5 + - - +
60A GLY 3.3 1.7 + - - -
62A TYR* 3.1 17.1 + - - +
170A ILE 5.5 1.8 - - - +
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Residues in contact with ARG 59 (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 VAL* 3.6 18.8 + - + +
38A ASP* 3.0 35.2 + - - +
39A SER* 4.8 4.5 - - - +
40A GLY 3.8 6.5 + - - +
41A CYS* 5.7 0.2 - - - -
58A ARG* 1.3 77.5 - - - +
60A GLY* 1.3 60.0 + - - +
62A TYR* 5.0 0.7 + - - -
16B TYR* 5.4 6.3 + - - -
22B HIS* 6.2 0.2 + - - -
28B TYR* 4.2 10.7 + - - -
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Residues in contact with GLY 60 (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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36A SER* 3.7 1.4 - - - -
37A VAL* 2.8 37.3 + - - +
58A ARG 3.3 2.6 + - - -
59A ARG* 1.3 76.9 - - - +
61A ASP* 1.3 65.2 + - - +
62A TYR* 4.1 9.6 - - - -
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Residues in contact with ASP 61 (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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11A PHE* 3.8 8.1 - - + -
35A ALA 3.9 3.4 - - - -
36A SER* 2.5 32.1 + - - -
60A GLY* 1.3 77.4 - - - +
62A TYR* 1.3 68.7 + - - +
63A ALA 4.1 1.1 - - - -
67A GLN* 3.9 8.2 - - - +
22B HIS* 4.8 9.7 - - - -
23B PRO* 3.7 38.1 - - + +
24B ASN* 3.8 11.2 - - - +
28B TYR* 6.1 0.7 - - - -
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Residues in contact with TYR 62 (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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11A PHE* 3.4 3.6 - - - -
34A SER* 3.1 9.4 - - - -
35A ALA 3.0 37.6 + - - +
37A VAL* 4.2 3.1 - - + -
56A PHE 4.7 1.9 + - - -
57A LEU* 3.5 34.1 - - + -
58A ARG* 3.1 40.0 + - - +
59A ARG 5.0 0.9 + - - -
60A GLY* 4.1 14.8 - - - -
61A ASP* 1.3 76.7 - - - +
63A ALA* 1.3 59.5 + - - +
64A ASP 3.2 2.5 - - - -
67A GLN* 3.5 44.6 - - + -
68A TRP* 3.6 27.4 - + + -
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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
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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