Contacts of the strand formed by residues 63 - 71 (chain A) in PDB entry 1GOG
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 GLN 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.8 30.7 - - + +
10A SER 5.6 0.2 + - - -
14A TRP* 5.3 0.6 - - - +
59A MET* 3.7 28.1 + - + +
61A THR* 3.4 28.9 + - - +
62A THR* 1.3 80.7 - - - +
64A ASN* 1.3 65.0 + - - +
65A VAL* 3.0 20.1 + - + +
120A PRO* 3.3 1.0 - - - +
121A ALA 2.8 30.2 + - - +
147A GLN* 3.6 17.2 - - + +
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Residues in contact with ASN 64 (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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62A THR* 5.5 1.2 - - - +
63A GLN* 1.3 74.2 - - - +
65A VAL* 1.3 59.1 + - - +
118A THR* 3.8 17.3 - - + -
119A ARG 4.3 3.4 - - - -
120A PRO* 4.0 15.2 - - - +
147A GLN* 3.0 9.3 + - + +
148A ALA* 3.0 39.2 + - + +
149A SER 5.1 0.6 - - - -
150A SER* 4.0 7.9 - - - +
151A TYR* 3.6 36.3 - - + +
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Residues in contact with VAL 65 (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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9A ILE* 4.5 0.2 - - + -
59A MET* 3.7 28.0 - - + -
63A GLN* 3.0 21.4 + - + +
64A ASN* 1.3 71.0 - - - +
66A ASN* 1.3 61.9 + - - +
67A GLY 4.0 0.9 - - - +
89A LEU* 4.1 15.0 - - + -
116A PHE* 3.8 28.2 - - + -
118A THR* 3.2 1.1 - - - -
119A ARG 2.8 38.7 + - - +
121A ALA* 4.0 7.2 - - + +
124A VAL* 4.5 1.8 - - + -
145A VAL* 3.7 25.8 - - + -
146A PHE 3.2 6.1 - - - +
147A GLN* 4.3 0.2 - - - +
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Residues in contact with ASN 66 (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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5A ILE* 3.4 41.5 + - + +
6A GLY* 3.2 20.4 + - - -
65A VAL* 1.3 73.2 - - - +
67A GLY* 1.3 59.9 + - - +
115A ASN* 3.7 0.2 - - - -
116A PHE* 3.1 41.9 + - - +
118A THR* 3.5 16.0 + - - +
146A PHE* 2.9 11.2 + - - +
147A GLN 3.6 6.1 - - - -
148A ALA* 3.7 27.7 - - - +
490A SER* 5.4 2.6 + - - -
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Residues in contact with GLY 67 (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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65A VAL* 4.2 1.4 - - - +
66A ASN* 1.3 83.1 + - - +
68A LEU* 1.3 63.7 + - - +
114A SER 3.0 13.9 - - - -
115A ASN* 4.4 4.3 - - - -
116A PHE* 3.4 13.5 - - - -
145A VAL* 3.5 8.5 - - - +
146A PHE* 2.8 34.2 + - - -
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Residues in contact with LEU 68 (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 PRO* 5.5 0.2 - - - +
67A GLY* 1.3 76.9 - - - +
69A SER* 1.3 74.5 - - - +
70A MET* 4.5 2.0 - - + +
87A VAL* 4.1 17.9 - - + -
105A TRP* 4.3 17.9 - - + -
113A TYR* 3.3 6.6 - - - +
114A SER* 2.9 49.6 + - - +
115A ASN* 5.2 0.5 + - - +
116A PHE* 5.1 1.8 - - + -
124A VAL* 4.0 25.8 - - + -
126A LEU* 4.4 15.5 - - + -
143A ILE* 4.3 17.7 - - + -
144A ASN 3.1 12.8 - - - +
145A VAL* 4.6 4.7 - - + -
146A PHE* 3.7 6.0 - - - -
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Residues in contact with SER 69 (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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68A LEU* 1.3 75.8 - - - +
70A MET* 1.3 64.2 + - - +
71A LEU 4.1 0.7 - - - -
111A THR* 3.8 9.3 - - - +
112A LYS 3.3 4.9 - - - -
113A TYR* 3.6 28.7 - - - -
142A GLU 4.6 0.2 - - - -
143A ILE* 3.4 11.3 - - - +
144A ASN* 2.9 41.5 + - - +
146A PHE* 3.4 19.4 - - - -
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Residues in contact with MET 70 (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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68A LEU* 4.6 3.6 - - + -
69A SER* 1.3 77.3 - - - +
71A LEU* 1.3 74.6 + - - +
72A PRO* 3.4 21.8 - - + +
81A TRP* 5.8 0.4 - - - -
82A ILE* 4.2 21.5 - - + +
105A TRP* 3.8 46.0 - - + -
111A THR* 4.2 2.0 - - - -
112A LYS* 2.8 46.8 + - + +
126A LEU* 4.3 7.2 - - + -
139A SER 4.6 2.9 - - - +
140A ILE* 4.1 30.5 - - + -
142A GLU 3.7 1.8 - - - -
143A ILE* 5.3 0.9 - - + -
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Residues in contact with LEU 71 (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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35A LYS* 3.4 45.8 - - + +
69A SER* 4.1 0.6 + - - -
70A MET* 1.3 75.4 - - - +
72A PRO* 1.3 72.1 - - + +
74A GLN* 3.4 22.2 - - + +
109A SER 4.4 0.4 - - - +
111A THR* 3.1 32.0 - - + +
140A ILE 3.8 0.9 - - - -
141A ALA* 2.9 30.4 + - + +
142A GLU* 2.9 35.5 + - + +
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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