Contacts of the strand formed by residues 76 - 82 (chain A) in PDB entry 6D6Q
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 LEU 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ILE* 1.3 82.6 - - - +
77A PHE* 1.3 65.9 + - - +
78A PHE* 3.1 48.5 - - + +
111A ARG* 3.0 35.9 + - + +
115A CYS* 5.9 1.3 - - - -
116A ILE* 3.1 37.5 - - + -
118A THR* 5.5 6.1 - - + -
132A ILE* 3.2 20.2 - - + +
134A VAL* 4.8 2.9 - - + -
157A LEU* 4.4 15.0 - - + -
41O A 3.7 6.8 - - - +
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Residues in contact with PHE 77 (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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75A ILE* 5.3 0.4 - - + -
76A LEU* 1.3 74.2 - - - +
78A PHE* 1.3 75.8 + - - +
79A ASN* 4.1 14.1 - - + -
131A GLN* 4.8 9.6 - - + +
132A ILE 2.9 9.6 + - - +
133A ARG* 3.1 60.5 - - + -
134A VAL 2.9 25.4 + - - -
135A ASP* 4.8 0.4 - - - -
41O A 3.1 70.2 - + + +
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Residues in contact with PHE 78 (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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76A LEU* 3.1 32.8 - - + -
77A PHE* 1.3 91.0 - - - +
79A ASN* 1.3 66.6 + - - +
103A ASN* 5.6 3.8 - - + +
106A MET* 3.5 26.5 - - + -
107A GLU* 3.8 48.3 + - + +
110A LEU* 3.3 46.7 - - + -
111A ARG* 4.2 19.0 - - + +
115A CYS* 5.9 0.2 - - - -
134A VAL* 3.1 31.0 - - + -
153A ALA* 4.9 0.4 - - + -
157A LEU* 5.3 2.5 - - + -
93B ARG* 4.8 8.3 + - - -
41O A 5.4 1.3 + - - +
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Residues in contact with ASN 79 (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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77A PHE* 4.1 12.9 - - + -
78A PHE* 1.3 80.3 - - - +
80A LEU* 1.3 79.3 + - - +
81A GLU* 4.0 20.7 + - - +
103A ASN* 4.2 10.9 + - - -
106A MET* 5.9 1.5 - - - -
133A ARG* 4.4 9.3 - - - +
134A VAL* 3.0 8.4 + - - +
135A ASP* 3.4 17.6 + - - +
136A LEU* 2.9 27.7 + - - +
93B ARG* 4.7 10.8 + - - +
85D GLY 5.2 0.6 + - - -
86D LEU* 4.0 15.0 - - - +
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Residues in contact with LEU 80 (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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55A VAL* 5.9 2.5 - - + -
79A ASN* 1.3 84.8 + - - +
81A GLU* 1.3 66.6 + - - +
82A LEU* 3.6 32.3 + - + -
99A LEU* 4.6 12.9 - - + +
102A LEU* 4.2 28.0 - - + -
103A ASN* 3.2 29.5 + - - +
106A MET* 4.9 8.1 - - + -
136A LEU* 3.3 21.8 - - + +
138A LEU* 5.2 3.1 - - + +
145A ILE* 4.6 3.8 - - + -
149A ALA* 3.8 29.6 - - + -
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Residues in contact with GLU 81 (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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79A ASN* 4.0 13.1 + - - +
80A LEU* 1.3 81.0 - - - +
82A LEU* 1.3 63.7 + - - +
83A SER* 3.6 3.8 + - - +
99A LEU* 5.6 2.2 - - + -
136A LEU 2.9 7.4 + - - +
137A HIS* 3.2 35.6 + - + +
138A LEU* 2.9 28.1 + - - +
81D ARG* 4.2 27.5 - - - +
85D GLY 4.1 5.9 - - - +
86D LEU* 3.1 32.2 - - - +
87D PRO* 4.7 6.1 - - - +
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Residues in contact with LEU 82 (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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80A LEU* 3.6 24.9 - - + -
81A GLU* 1.3 70.8 - - - +
83A SER* 1.3 67.2 + - - +
84A GLN 3.5 1.2 + - - -
90A PHE* 3.8 37.0 - - + +
95A GLN* 4.8 0.9 - - + +
98A LEU* 3.9 26.2 - - + -
99A LEU* 3.4 38.4 - - + +
102A LEU* 5.0 2.7 - - + -
138A LEU* 3.3 32.1 - - + -
145A ILE* 4.7 9.2 - - + -
81D ARG* 4.3 8.5 + - - +
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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