Contacts of the helix formed by residues 77 - 92 (chain A) in PDB entry 4P8V
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 SER 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN* 2.6 26.5 + - - -
47A THR* 6.6 0.2 - - - -
48A PRO* 6.1 4.9 - - - -
75A ASP* 2.8 16.1 + - - -
76A LYS* 1.3 81.6 - - - +
78A GLU* 1.3 64.5 + - - +
79A VAL 3.4 2.7 - - - -
80A MET* 3.1 31.6 + - - +
81A LEU* 3.0 20.4 + - - +
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Residues in contact with GLU 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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73A ILE* 3.3 42.1 + - + +
75A ASP* 3.0 24.0 + - - +
76A LYS 3.4 1.6 + - - -
77A SER* 1.3 77.1 - - - +
79A VAL* 1.3 70.5 + - + +
81A LEU* 3.1 22.2 + - - +
82A TYR* 2.7 43.7 + - + +
131A PHE* 4.6 3.8 - - - -
135A HIS* 5.2 0.7 + - - -
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Residues in contact with VAL 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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76A LYS 5.4 0.4 + - - -
77A SER 3.4 0.6 - - - -
78A GLU* 1.3 86.2 - - + +
80A MET* 1.3 61.9 + - + +
82A TYR* 3.3 30.2 + - + +
83A GLN* 3.4 18.8 + - + +
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Residues in contact with MET 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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48A PRO* 5.9 0.4 - - - -
76A LYS 4.8 3.1 - - - +
77A SER* 3.1 36.3 + - - +
79A VAL* 1.3 77.3 - - + +
81A LEU* 1.3 64.8 + - - +
83A GLN* 3.2 12.9 + - + +
84A THR* 3.0 26.6 + - - +
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Residues in contact with LEU 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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33A PHE* 4.2 10.8 - - + -
48A PRO* 3.9 28.4 - - + +
61A TYR* 3.5 46.4 - - + -
73A ILE* 4.1 22.2 - - + -
75A ASP* 5.1 2.0 - - - +
77A SER 3.0 11.7 + - - +
78A GLU* 3.2 13.5 - - - +
80A MET* 1.3 75.9 - - - +
82A TYR* 1.3 63.1 + - + +
84A THR* 3.1 7.4 + - - -
85A ILE* 2.8 48.8 + - + +
137A PHE* 4.6 1.6 - - + -
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Residues in contact with TYR 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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73A ILE* 3.6 9.1 - - + +
78A GLU* 2.7 52.7 + - + +
79A VAL* 3.3 22.8 + - + +
80A MET 3.2 1.0 - - - -
81A LEU* 1.3 79.5 - - + +
83A GLN* 1.3 65.5 + - - +
85A ILE* 3.3 13.8 + - + +
86A ASN* 3.1 36.1 + - - +
131A PHE* 3.2 21.0 - - - -
135A HIS* 3.5 55.1 - + + +
137A PHE* 4.1 11.9 - + - -
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Residues in contact with GLN 83 (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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49A GLU* 5.7 1.1 - - - +
79A VAL* 3.4 17.8 + - + +
80A MET* 3.2 15.6 + - + +
82A TYR* 1.3 80.1 - - - +
84A THR* 1.3 59.0 + - - +
86A ASN* 3.3 12.9 + - - +
87A SER* 2.9 28.3 + - - -
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Residues in contact with THR 84 (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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48A PRO* 3.5 44.6 - - + +
49A GLU* 2.7 32.4 + - - +
80A MET* 3.0 14.1 + - - +
81A LEU* 3.5 6.5 - - - -
83A GLN* 1.3 74.9 - - - +
85A ILE* 1.3 60.6 + - - +
87A SER* 4.3 4.3 - - - -
88A LEU* 2.8 52.3 + - + +
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Residues in contact with ILE 85 (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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81A LEU* 2.8 43.1 + - + +
82A TYR* 3.6 13.2 - - + +
84A THR* 1.3 73.2 - - - +
86A ASN* 1.3 68.6 + - - +
88A LEU* 3.8 2.7 - - + +
89A LYS* 3.0 35.9 + - + +
97A ILE* 4.1 24.2 - - + -
135A HIS 4.0 8.7 - - - +
136A ASN* 3.7 22.7 - - + +
137A PHE* 3.5 41.1 - - + -
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Residues in contact with ASN 86 (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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82A TYR* 3.1 23.8 + - - +
83A GLN* 3.8 12.9 + - - +
85A ILE* 1.3 75.6 - - - +
87A SER* 1.3 58.6 + - - +
89A LYS* 4.0 1.0 - - - +
90A THR* 2.7 34.4 + - - +
135A HIS 4.7 1.0 - - - +
136A ASN* 3.0 37.4 + - - +
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Residues in contact with SER 87 (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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49A GLU* 5.4 4.0 + - - -
83A GLN 2.9 18.3 + - - -
84A THR* 3.1 8.0 + - - -
86A ASN* 1.3 75.2 - - - +
88A LEU* 1.3 66.7 + - - +
90A THR* 3.2 7.3 + - - -
91A LYS* 2.6 55.9 + - - +
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Residues in contact with LEU 88 (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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48A PRO* 5.0 0.4 - - + +
51A ILE* 3.7 38.4 - - + +
53A PRO* 3.8 28.8 - - + +
59A LEU* 3.9 23.8 - - + -
84A THR* 2.8 44.9 + - + +
85A ILE* 3.8 4.9 - - + +
87A SER* 1.3 74.0 - - - +
89A LYS* 1.3 56.9 + - - +
91A LYS* 3.3 7.4 + - + +
92A ASN* 2.9 30.0 + - - +
95A LEU* 3.8 12.6 - - + +
97A ILE* 4.2 9.2 - - + -
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Residues in contact with LYS 89 (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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85A ILE* 3.0 18.3 + - + +
86A ASN 4.3 2.2 - - - +
88A LEU* 1.3 72.4 - - - +
90A THR* 1.3 63.2 + - - +
92A ASN 3.8 6.7 - - - +
93A PRO* 3.3 27.8 - - + +
95A LEU* 4.0 17.7 - - + +
97A ILE* 3.8 25.4 - - + -
136A ASN* 2.8 51.8 + - - +
137A PHE 4.8 0.2 + - - -
138A ASP* 2.8 36.2 + - - +
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Residues in contact with THR 90 (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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86A ASN* 2.7 23.8 + - - +
87A SER* 3.2 6.4 + - - -
89A LYS* 1.3 77.4 - - - +
91A LYS* 1.3 65.7 + - + +
93A PRO* 3.8 12.1 - - - +
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Residues in contact with LYS 91 (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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53A PRO* 3.9 28.7 - - + -
54A PHE* 3.3 19.5 - - + -
87A SER* 2.6 42.4 + - - +
88A LEU* 3.7 9.0 - - + +
90A THR* 1.3 80.7 - - + +
92A ASN* 1.3 57.2 + - - +
93A PRO* 3.6 5.6 - - - +
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Residues in contact with ASN 92 (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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53A PRO* 3.0 30.2 + - + +
54A PHE* 3.5 33.0 - - + +
56A CYS 4.6 3.4 + - - -
57A SER* 6.0 0.4 - - - +
88A LEU 2.9 11.3 + - - +
89A LYS* 3.4 10.3 - - - +
91A LYS* 1.3 76.1 - - - +
93A PRO* 1.3 66.6 - - - +
94A LYS* 3.0 24.6 + - - +
95A LEU* 3.0 35.7 + - + +
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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