Contacts of the strand formed by residues 99 - 108 (chain A) in PDB entry 1HS6
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LYS* 5.0 6.3 - - - +
41A THR* 3.8 23.0 - - + +
42A VAL 3.0 13.2 - - - +
43A GLN* 3.5 26.5 - - + +
94A LEU* 4.6 4.5 - - - +
97A ASN 3.8 8.5 - - - +
98A GLN* 1.3 80.8 + - - +
100A ILE* 1.3 63.1 + - - +
101A VAL* 5.8 0.4 - - - +
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Residues in contact with ILE 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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41A THR* 3.6 3.2 - - - +
42A VAL* 2.9 42.5 + - + +
52A LEU* 4.7 1.8 - - + -
66A ILE* 4.3 18.6 - - + -
67A ASN* 5.1 8.3 - - - +
90A LEU* 4.5 14.8 - - + -
91A PRO* 5.6 5.8 - - + -
92A ILE* 5.9 8.5 - - + +
94A LEU* 3.5 32.1 - - + -
99A GLU* 1.3 76.0 - - - +
101A VAL* 1.3 67.6 + - - +
102A ILE* 3.0 42.8 - - + -
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Residues in contact with VAL 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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39A ALA* 4.6 13.7 - - + -
40A LEU 3.3 11.9 - - - +
41A THR* 4.1 17.3 - - + +
66A ILE* 3.2 26.2 - - - +
67A ASN* 4.6 3.6 + - - +
100A ILE* 1.3 79.3 - - - +
102A ILE* 1.3 69.5 + - - +
103A GLU* 4.2 3.7 + - + +
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Residues in contact with ILE 102 (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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38A ALA 3.1 4.7 - - - +
40A LEU* 2.8 44.9 + - + +
42A VAL* 4.3 10.8 - - + -
52A LEU* 3.9 27.1 - - + -
54A LEU* 6.1 1.1 - - + -
64A VAL* 3.8 27.8 - - + -
65A VAL 3.8 1.8 - - - -
66A ILE* 3.9 13.7 - - + -
88A ILE* 4.1 16.2 - - + -
90A LEU* 4.3 6.5 - - + -
100A ILE* 3.0 35.4 - - + -
101A VAL* 1.3 75.1 - - - +
103A GLU* 1.3 59.2 + - - +
104A ILE* 4.5 6.8 - - + +
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Residues in contact with GLU 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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24A ARG* 3.9 18.3 + - - -
37A THR* 3.8 32.0 + - + +
38A ALA 3.5 2.2 - - - -
39A ALA* 4.0 18.5 - - + +
63A LYS* 4.0 5.5 + - - +
64A VAL* 3.5 3.3 - - - +
65A VAL* 2.8 59.1 + - + +
101A VAL* 4.1 4.6 - - + -
102A ILE* 1.3 70.6 - - - +
104A ILE* 1.3 62.8 + - - +
105A SER* 4.2 2.2 + - - -
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Residues in contact with ILE 104 (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 THR* 2.8 12.3 - - - -
38A ALA* 2.6 48.0 + - + +
40A LEU* 4.3 11.9 - - + -
54A LEU* 3.8 29.4 - - + -
61A ILE* 4.0 18.6 - - + -
63A LYS 3.7 7.0 - - - +
64A VAL* 3.9 15.3 - - + -
86A MET* 4.4 2.0 - - + -
88A ILE* 4.3 6.3 - - + -
102A ILE* 4.5 11.0 - - + +
103A GLU* 1.3 78.9 - - - +
105A SER* 1.3 62.5 - - - +
106A PHE* 3.4 8.4 - - + -
145A PRO* 3.8 29.4 - - + -
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Residues in contact with SER 105 (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 GLY 3.4 5.2 + - - -
37A THR* 3.6 16.7 - - - +
61A ILE* 3.4 6.8 - - - +
62A GLU* 2.6 48.5 + - - -
63A LYS* 2.7 49.0 + - - +
103A GLU* 4.2 1.6 + - - -
104A ILE* 1.3 68.2 - - - +
106A PHE* 1.3 55.6 + - - +
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Residues in contact with PHE 106 (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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23A LEU* 3.9 17.9 - - + -
25A CYS* 4.8 4.0 - - + -
34A LEU* 4.2 18.6 - - + -
35A THR* 3.4 5.7 - - - +
36A GLY* 2.8 52.0 + - - +
37A THR 3.6 23.3 - - - -
38A ALA* 3.6 15.3 - - + -
59A LEU* 4.9 4.3 - - + -
60A THR 3.2 9.4 - - - +
61A ILE* 4.5 8.1 - - + -
62A GLU* 4.4 3.1 - - - +
104A ILE* 3.4 21.8 - - + -
105A SER* 1.3 75.4 - - - +
107A GLU* 1.3 69.8 + - - +
108A THR* 4.5 1.6 - - + -
143A ILE* 3.2 29.8 - - + -
144A LEU* 4.1 8.3 - - + -
145A PRO* 4.3 11.4 - - + -
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Residues in contact with GLU 107 (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 THR* 4.4 15.2 - - + +
34A LEU 3.4 3.1 - - - +
35A THR* 3.6 28.4 + - + +
59A LEU* 3.8 2.4 - - - +
60A THR* 2.7 61.9 + - + +
106A PHE* 1.3 76.5 - - - +
108A THR* 1.3 66.0 + - - +
802A YB 3.8 12.2 - - - -
803A YB 2.2 30.0 - - - -
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Residues in contact with THR 108 (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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32A ARG 4.8 0.3 + - - -
33A THR* 3.3 24.8 - - - +
34A LEU* 3.0 46.0 + - + +
59A LEU* 3.7 7.4 - - + -
60A THR* 5.7 1.1 - - - -
106A PHE* 4.5 1.3 - - + -
107A GLU* 1.3 79.0 - - - +
109A SER* 1.3 65.5 + - - +
110A PRO* 4.4 0.5 - - - +
112A SER* 4.6 3.1 - - - -
115A LEU* 4.5 8.6 - - + +
142A ALA 3.6 20.4 - - - +
143A ILE* 3.2 32.5 - - + +
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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