Contacts of the strand formed by residues 98 - 107 (chain B) in PDB entry 3HQL
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 VAL 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.8 30.5 - - + -
67B TRP* 4.0 15.9 - - + -
90B LEU* 3.6 26.0 - - + -
93B CYS* 4.0 10.5 - - - -
95B LYS* 4.7 6.3 - - + -
97B GLU* 1.3 80.6 - - - +
99B ARG* 1.3 65.8 + - - +
100B ALA* 5.4 0.4 - - + -
123B TYR 3.6 0.9 - - - +
124B ARG* 3.7 0.6 - - - -
125B PHE* 2.8 34.2 + - + +
163B VAL* 4.7 13.2 - - + -
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN* 6.1 1.0 - - - +
97B GLU* 5.8 2.5 - - + +
98B VAL* 1.3 76.0 - - - +
100B ALA* 1.3 60.4 + - - +
122B ALA* 4.2 17.1 + - + +
123B TYR 3.3 6.7 - - - +
124B ARG* 4.0 41.2 - - + +
163B VAL* 3.7 22.1 - - - +
164B VAL 3.7 18.1 + - - +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B TRP* 4.0 9.4 - - + -
88B LEU* 5.4 0.2 - - + -
98B VAL 4.0 0.9 + - - +
99B ARG* 1.3 75.0 - - - +
101B LYS* 1.3 60.0 - - - +
102B PHE* 4.1 3.8 - - - -
121B ARG 4.4 0.2 - - - +
122B ALA* 3.8 6.4 - - - +
123B TYR* 2.9 28.2 + - - +
125B PHE* 3.9 23.4 - - + -
161B VAL* 4.0 15.0 - - + -
162B SER 3.3 10.8 - - - +
163B VAL* 4.0 15.5 - - + -
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA* 1.3 73.4 - - - +
102B PHE* 1.3 64.3 + - - +
119B SER* 3.4 12.3 - - - +
120B GLN 5.0 2.7 + - - -
121B ARG* 3.6 11.9 - - - +
122B ALA* 3.4 36.1 - - + +
161B VAL* 3.4 4.9 - - - +
162B SER* 2.9 47.6 + - - +
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 3.8 19.5 - - + -
100B ALA 4.1 7.4 - - - -
101B LYS* 1.3 79.8 - - - +
103B LYS* 1.3 61.3 + - - +
104B PHE* 3.6 30.1 - + + -
118B GLU* 3.4 2.1 - - - +
119B SER* 2.9 50.4 + - - -
123B TYR* 4.3 9.9 - + + -
125B PHE* 4.2 14.1 - + - -
131B TRP* 3.9 33.9 - - + -
132B GLY* 4.0 4.7 - - - -
133B PHE* 3.7 28.7 - + - -
160B GLU 3.2 11.4 - - - +
161B VAL* 4.5 1.1 - - + -
98D VAL* 3.9 13.7 - - + -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PHE* 1.3 76.2 - - - +
104B PHE* 1.3 72.9 + - - +
113B GLU* 3.7 19.2 + - - +
116B ALA* 3.6 23.6 - - - +
117B MET 3.3 13.0 - - - +
118B GLU* 3.9 25.4 - - + +
158B PHE 3.8 0.9 - - - +
159B CYS* 3.3 3.8 - - - -
160B GLU* 2.9 56.2 + - + +
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.1 9.2 - - + -
86B LEU* 3.5 47.8 - - + -
87B TYR 4.0 1.8 - - - -
88B LEU* 3.7 25.4 - - + -
102B PHE* 3.6 23.6 - + - -
103B LYS* 1.3 83.3 - - - +
105B SER* 1.3 62.4 + - - +
116B ALA* 3.2 3.5 - - - +
117B MET 2.9 32.2 + - - +
132B GLY* 4.2 1.6 - - - -
133B PHE* 3.5 30.5 - + - -
136B PHE* 3.7 14.7 - - + -
157B LEU* 6.4 0.4 - - + -
158B PHE 3.3 4.9 - - - +
159B CYS* 3.4 31.6 - - + -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 5.5 0.7 - - - -
104B PHE* 1.3 76.6 - - - +
106B ILE* 1.3 66.3 + - - +
107B LEU* 4.3 0.3 - - - +
113B GLU* 3.1 41.8 + - - +
114B THR 3.6 12.1 - - - -
116B ALA* 3.8 13.9 - - - +
136B PHE* 4.2 5.3 - - - -
157B LEU* 3.4 7.3 - - - +
158B PHE* 2.9 39.0 + - - +
160B GLU* 4.8 0.3 + - - -
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 6.3 0.4 - - + -
105B SER* 1.3 77.7 - - - +
107B LEU* 1.3 72.4 + - - +
112B GLU 3.5 0.2 - - - +
113B GLU* 3.6 0.3 - - - -
114B THR* 2.8 44.0 + - + +
115B LYS* 4.4 7.0 - - + -
136B PHE* 3.9 24.0 - - + -
137B ILE* 3.4 37.0 - - + -
142B LEU* 4.4 7.2 - - + -
149B LEU* 4.0 25.6 - - + +
155B LEU* 4.0 17.3 - - + -
156B THR 3.5 9.9 - - - +
157B LEU* 3.9 8.3 - - + -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B MET* 4.0 18.4 - - + -
105B SER* 4.3 0.2 - - - +
106B ILE* 1.3 84.2 - - - +
108B ASN* 1.3 67.4 + - - +
111B GLY* 3.9 22.4 - - - +
112B GLU 3.3 2.0 - - - +
113B GLU* 3.5 35.7 - - + -
149B LEU* 4.4 7.6 - - - +
151B PRO* 5.3 2.6 - - - +
156B THR* 2.9 45.4 + - + +
158B PHE* 3.8 26.0 - - + -
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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