Contacts of the strand formed by residues 94 - 103 (chain A) in PDB entry 5HH0
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.7 22.8 + - + +
72A LYS* 3.3 21.3 - - - +
73A ASN* 4.0 5.5 - - + +
92A ASP 3.8 9.6 - - - +
93A THR* 1.3 81.0 - - - +
95A VAL* 1.3 68.5 + - - +
127A THR 5.3 0.3 - - - +
128A ALA* 3.7 21.1 - - - +
131A HIS* 3.1 17.3 + - + +
132A CYS* 3.8 17.9 - - + -
133A LYS 2.9 24.8 + - - -
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Residues in contact with VAL 95 (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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70A GLU 3.7 0.5 - - - +
71A ILE* 3.4 3.1 - - - +
72A LYS* 2.8 47.5 + - + +
73A ASN 4.6 1.8 - - - +
74A ARG* 4.7 3.4 - - + -
77A ILE* 3.8 32.8 - - + -
84A ILE* 4.5 2.0 - - + -
85A LEU* 3.6 27.8 - - + -
94A GLN* 1.3 80.1 - - - +
96A ALA* 1.3 60.3 + - - +
132A CYS* 3.7 5.2 - - - -
134A ALA* 3.4 20.9 - - + +
136A TYR* 3.8 19.5 - - + -
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Residues in contact with ALA 96 (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 ALA* 5.2 1.1 - - + -
70A GLU 3.4 8.1 - - - +
71A ILE* 4.3 10.5 - - + -
95A VAL* 1.3 75.1 - - - +
97A TYR* 1.3 62.1 + - - +
120A LEU* 5.1 7.0 - - + -
124A ILE* 3.7 30.5 - - + -
132A CYS* 3.8 3.6 - - - -
134A ALA 2.9 10.5 + - - +
135A ILE* 3.2 9.8 - - + +
136A TYR* 2.9 28.5 + - - +
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Residues in contact with TYR 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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69A ALA* 3.2 4.7 - - - -
70A GLU* 2.9 34.4 + - + +
72A LYS* 4.0 19.0 - - + +
95A VAL 4.2 0.4 - - - -
96A ALA* 1.3 72.8 - - - +
98A ILE* 1.3 71.5 + - - +
99A LEU* 3.4 32.2 + - + +
136A TYR* 3.3 46.6 - + + +
137A LEU* 3.9 13.5 - - - -
138A HIS* 2.7 45.9 + + - +
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Residues in contact with ILE 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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67A ILE* 4.3 10.8 - - + -
68A VAL 3.6 6.3 - - - +
69A ALA* 4.3 0.7 - - + -
97A TYR* 1.3 87.5 + - - +
99A LEU* 1.3 60.4 + - - +
100A SER* 3.6 28.3 - - - +
101A LEU* 4.0 11.0 - - + +
117A LEU* 4.4 11.9 - - + -
120A LEU* 3.9 26.5 - - + -
135A ILE* 3.9 23.3 - - + -
136A TYR 3.0 8.3 + - - +
137A LEU* 4.0 34.6 - - + +
138A HIS 4.8 1.2 + - - -
150A TYR* 4.7 6.7 - - + +
155A PHE* 4.7 0.9 - - + -
201A COA 5.4 3.4 - - - -
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Residues in contact with LEU 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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38A TYR* 4.5 11.8 + - - -
42A TRP* 4.3 23.7 - - + +
46A ILE* 4.2 17.7 - - + -
52A PHE* 3.8 24.7 - - + -
68A VAL* 2.8 16.2 + - + +
69A ALA* 3.9 5.4 - - - -
70A GLU* 3.7 25.8 - - + +
97A TYR* 3.5 41.4 + - + +
98A ILE* 1.3 72.9 - - - +
100A SER* 1.3 62.3 + - - +
201A COA 4.4 5.9 - - - -
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Residues in contact with SER 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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30A CYS* 4.1 8.3 - - - -
33A TRP* 4.0 21.7 - - - -
38A TYR* 6.4 0.2 - - - -
42A TRP* 5.0 7.0 - - - -
66A MET* 4.1 21.7 - - - +
67A ILE* 3.3 3.7 - - - -
68A VAL* 2.8 34.0 + - - +
98A ILE* 3.4 7.0 - - - +
99A LEU* 1.3 83.3 - - - +
101A LEU* 1.3 61.5 + - - +
201A COA 3.6 11.0 - - - -
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Residues in contact with LEU 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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66A MET 3.4 16.4 - - - +
67A ILE* 3.9 16.2 - - + -
98A ILE* 4.1 9.0 - - + -
100A SER* 1.3 77.3 + - - +
102A GLY* 1.3 60.5 + - - +
113A GLY* 4.5 9.0 - - - +
116A LEU* 3.9 30.1 - - + -
117A LEU* 5.0 5.2 - - + -
149A PHE* 3.9 22.4 - - + -
150A TYR* 3.2 34.5 - - + +
201A COA 2.9 49.2 - - + +
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Residues in contact with GLY 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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33A TRP* 3.3 28.0 - - - -
65A GLY* 3.2 2.4 - - - -
66A MET 2.9 33.1 + - - +
101A LEU* 1.3 76.4 - - - +
103A VAL* 1.3 66.2 + - - +
116A LEU* 4.3 0.5 - - - +
201A COA 3.3 11.2 - - - -
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Residues in contact with VAL 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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33A TRP* 3.4 6.4 + - - -
64A VAL 3.4 10.5 - - - +
65A GLY* 4.4 0.9 - - - -
102A GLY* 1.3 81.4 - - - +
104A VAL* 1.3 71.2 + - - +
107A PHE* 3.8 22.0 - - + +
108A ARG* 2.8 35.5 + - + +
112A ILE* 3.7 27.4 - - + -
113A GLY* 3.9 9.0 - - - +
116A LEU* 4.4 2.7 - - + -
201A COA 2.7 45.8 + - + +
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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