Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 3HIG
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 GLU 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A MET* 3.8 9.5 - - - +
75A LEU* 3.0 43.7 + - + +
77A PRO* 6.0 1.2 - - - +
94A VAL* 3.9 12.9 + - + +
95A ARG* 1.3 79.3 - - - +
97A ALA* 1.3 63.7 + - - +
115A ALA* 4.0 4.2 - - + +
116A VAL 3.3 12.3 - - - +
117A GLY* 4.6 0.2 - - - -
119A LEU* 4.1 8.0 - - - +
124A TYR* 2.6 33.9 + - - +
126A ARG* 2.9 41.8 + - - -
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Residues in contact with ALA 97 (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 LEU* 3.8 15.0 - - + -
44A VAL* 3.7 32.8 - - + -
72A ILE* 4.0 8.5 - - + -
73A GLU 3.3 10.8 - - - +
74A MET* 4.3 0.2 - - - +
75A LEU* 4.0 4.3 - - - -
96A GLU* 1.3 73.9 - - - +
98A ARG* 1.3 59.7 + - - +
115A ALA* 3.3 6.6 - - - +
116A VAL* 2.8 33.5 + - + +
119A LEU* 4.2 2.0 - - + +
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Residues in contact with ARG 98 (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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71A LEU* 3.7 10.7 - - + +
72A ILE* 3.2 7.8 - - - +
73A GLU* 2.6 67.4 + - + +
75A LEU* 3.8 16.3 - - + +
97A ALA* 1.3 73.5 - - - +
99A ALA* 1.3 61.1 + - - +
100A VAL* 3.6 8.4 - - + +
113A GLU* 2.8 38.6 + - - +
114A PHE 3.6 4.5 - - - -
128A LEU* 3.7 23.3 - - + -
329A ARG* 3.9 12.5 - - - +
331A SER* 3.5 19.2 + - - -
636A SER* 6.1 1.0 - - - -
637A ILE* 3.8 25.7 - - - +
638A TYR* 4.6 1.8 - - - -
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Residues in contact with ALA 99 (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 VAL* 4.9 2.9 - - + -
48A LEU* 3.8 29.4 - - + -
69A VAL* 4.7 1.8 - - + -
71A LEU 3.3 7.0 - - - +
72A ILE* 4.6 5.6 - - + -
97A ALA 3.9 0.2 + - - -
98A ARG* 1.3 74.9 - - - +
100A VAL* 1.3 63.0 + - - +
101A ILE* 3.8 3.8 + - + -
112A THR 4.0 0.3 - - - +
113A GLU* 3.4 3.1 - - - -
114A PHE* 2.9 46.7 + - + +
116A VAL* 4.3 13.7 - - + -
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Residues in contact with VAL 100 (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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69A VAL* 3.6 3.3 - - - -
70A PHE* 2.8 34.1 + - + -
71A LEU* 2.8 34.8 + - + +
98A ARG* 3.6 16.8 - - + +
99A ALA* 1.3 72.6 - - - +
101A ILE* 1.3 54.9 + - - +
102A PHE* 4.2 14.4 - - + -
111A VAL* 3.5 31.0 - - + -
112A THR 3.9 2.5 - - - -
113A GLU* 3.4 30.5 - - + +
637A ILE* 4.3 7.0 - - + -
638A TYR* 3.5 7.0 - - - +
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Residues in contact with ILE 101 (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 LEU* 4.5 11.7 - - + -
54A LEU* 4.5 11.7 - - + -
56A LEU* 4.2 9.9 - - + -
68A THR 3.4 13.2 - - - +
69A VAL* 4.1 18.4 - - + -
99A ALA* 4.7 2.9 - - + +
100A VAL* 1.3 77.3 - - - +
102A PHE* 1.3 70.7 - - - +
103A PHE* 3.5 33.6 + - + -
111A VAL* 3.5 2.4 - - - +
112A THR 2.9 37.8 + - - +
114A PHE* 3.4 31.4 - - + -
125A MET* 4.1 12.3 - - + -
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LYS 3.4 1.3 - - - +
67A ASN* 3.2 5.4 - - - -
68A THR* 2.8 50.7 + - + +
70A PHE* 3.5 50.9 - + + -
100A VAL* 4.2 8.3 - - + -
101A ILE* 1.3 73.8 - - - +
103A PHE* 1.3 60.0 + - - +
104A GLY 3.3 1.9 + - - -
110A ASN 4.0 4.3 - - - -
111A VAL* 3.8 22.7 - - + +
138A TRP* 3.9 11.2 - + + -
141A ARG* 3.6 43.3 - - + -
142A PRO* 3.9 16.8 - - + -
144A SER* 5.3 6.1 - - - -
637A ILE* 5.9 0.2 - - + -
638A TYR* 5.7 0.2 - + - -
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Residues in contact with PHE 103 (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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54A LEU* 4.0 22.9 - - + -
67A ASN* 3.3 29.2 - - - +
101A ILE* 3.5 27.5 + - + -
102A PHE* 1.3 67.9 - - - +
104A GLY* 1.3 59.9 + - - +
105A ASP 3.4 0.4 - - - -
106A GLN* 3.5 20.9 - - - +
109A PRO* 3.2 7.1 - - - +
110A ASN* 2.8 39.3 + - - +
112A THR* 3.6 35.9 - - - -
114A PHE* 4.0 12.3 - + - -
138A TRP* 3.7 1.1 - - - -
1C NAG 3.7 23.3 - - - -
2C NAG 4.0 20.0 - - + -
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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