Contacts of the strand formed by residues 108 - 122 (chain A) in PDB entry 2VPA
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.4 11.2 - - - -
99A LEU* 2.8 50.9 + - - +
106A GLU 3.3 10.9 + - - -
107A LEU* 1.3 77.1 - - - +
109A VAL* 1.3 59.9 + - - +
175A ASN* 6.1 1.0 - - - -
180A ALA* 4.6 1.6 - - - +
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Residues in contact with VAL 109 (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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95A ILE* 3.7 23.8 - - + -
96A GLY 4.0 1.8 - - - +
97A GLN 3.5 19.1 - - - +
98A PHE* 3.9 30.7 - - + +
99A LEU* 5.0 0.9 - - - -
108A SER* 1.3 81.0 - - - +
110A GLN* 1.3 77.5 + - - +
111A TYR* 3.5 21.9 + - + -
175A ASN* 4.0 1.9 - - - +
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Residues in contact with GLN 110 (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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95A ILE* 3.6 3.6 - - - +
96A GLY* 2.9 27.2 + - - -
97A GLN* 2.8 50.0 + - - +
99A LEU* 3.9 19.7 - - + +
109A VAL* 1.3 77.1 - - - +
111A TYR* 1.3 60.3 + - - +
175A ASN 3.3 7.0 - - - +
176A TRP* 3.5 42.1 - - + +
177A ALA 2.9 28.1 + - - +
178A GLU* 4.5 4.4 - - - +
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Residues in contact with TYR 111 (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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20A ASN* 3.7 21.0 + - - +
94A GLU 3.3 8.7 - - - +
95A ILE* 4.3 13.7 - - + -
109A VAL* 3.6 21.1 - - + +
110A GLN* 1.3 76.8 - - - +
112A ARG* 1.3 76.2 + - - +
113A SER* 4.1 12.3 - - - -
173A LYS* 3.7 45.3 + - + -
174A GLU* 3.4 0.9 - - - +
175A ASN* 2.9 66.3 + - + +
176A TRP* 3.5 3.4 - - - -
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Residues in contact with ARG 112 (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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26A TRP* 3.7 14.1 - - + +
30A LEU* 3.5 16.8 - - + -
33A ARG* 3.9 12.2 - - - +
93A SER* 3.0 7.4 - - - -
94A GLU* 2.8 60.1 + - + +
111A TYR* 1.3 81.3 - - - +
113A SER* 1.3 60.1 + - - +
173A LYS 3.4 6.5 - - - -
174A GLU* 2.9 28.7 + - + +
176A TRP* 3.5 54.7 - - + +
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Residues in contact with SER 113 (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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26A TRP* 4.3 1.2 - - - -
91A GLU* 2.6 30.4 + - - +
92A VAL 3.4 5.2 - - - -
93A SER* 4.1 2.7 - - - -
111A TYR* 4.1 14.1 - - - -
112A ARG* 1.3 75.7 - - - +
114A VAL* 1.3 66.1 + - - +
115A MET* 5.3 2.6 - - - +
171A SER 3.9 0.7 - - - +
172A GLY* 3.5 1.4 - - - -
173A LYS* 2.9 38.8 + - - +
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Residues in contact with VAL 114 (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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26A TRP* 3.8 22.9 - - + -
27A ILE* 3.7 36.3 - - + -
30A LEU* 3.9 19.7 - - + -
31A LEU* 4.3 8.5 - - + -
90A LEU 3.6 0.5 - - - +
91A GLU* 3.2 8.3 - - - +
92A VAL 2.9 32.8 + - - +
113A SER* 1.3 80.3 - - - +
115A MET* 1.3 67.8 + - - +
116A VAL* 3.8 23.3 - - + -
170A TRP* 4.6 0.7 - - + -
171A SER 3.3 6.5 - - - +
172A GLY* 4.1 1.1 - - - -
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Residues in contact with MET 115 (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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89A THR* 4.4 11.2 - - + -
90A LEU 3.4 4.3 - - - -
91A GLU* 4.6 12.6 - - + -
113A SER* 4.4 2.4 + - - +
114A VAL* 1.3 74.4 - - - +
116A VAL* 1.3 60.8 + - - +
117A PHE* 3.8 35.4 - - + -
170A TRP* 3.2 5.4 - - - +
171A SER* 2.9 40.8 + - - +
173A LYS* 6.3 2.9 - - + -
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Residues in contact with VAL 116 (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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31A LEU* 4.1 19.1 - - + -
68A LEU* 3.8 11.4 - - + -
88A ALA 3.8 1.4 - - - +
89A THR* 3.3 7.8 - - - +
90A LEU* 2.8 54.7 + - + +
114A VAL* 3.8 18.6 - - + -
115A MET* 1.3 78.0 - - - +
117A PHE* 1.3 63.0 + - - +
165A LEU* 4.3 9.7 - - + +
167A ILE* 3.7 38.8 - - + -
169A ARG 3.7 3.4 - - - +
170A TRP* 4.2 5.4 - - + -
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Residues in contact with PHE 117 (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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88A ALA 3.8 2.5 - - - -
89A THR* 3.5 36.1 - - + -
115A MET* 3.8 37.0 - - + -
116A VAL* 1.3 75.9 - - - +
118A GLY* 1.3 57.8 + - - +
167A ILE* 3.9 1.0 - - - -
168A ASP* 2.9 23.1 + - - +
169A ARG* 2.9 67.8 + - + +
170A TRP* 4.7 0.7 - - - -
171A SER* 4.6 12.3 - - - -
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Residues in contact with GLY 118 (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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87A PRO* 3.4 7.1 - - - +
88A ALA 2.9 30.9 + - - -
117A PHE* 1.3 75.6 - - - +
119A THR* 1.3 64.3 + - - -
165A LEU* 3.7 7.6 - - - +
166A SER 3.3 13.9 - - - -
168A ASP* 3.6 13.7 - - - -
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Residues in contact with THR 119 (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 GLY* 4.2 8.3 - - - -
86A HIS 3.5 24.0 - - - +
87A PRO* 4.6 5.5 - - + +
118A GLY* 1.3 75.4 + - - -
120A ALA* 1.3 66.0 - - - +
121A ARG* 4.1 3.1 + - + +
164A SER 3.6 1.9 - - - +
165A LEU* 4.0 2.6 - - - +
166A SER* 2.9 39.6 + - - -
168A ASP* 4.3 8.7 + - - -
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Residues in contact with ALA 120 (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 TYR* 3.5 20.9 - - + +
85A GLY* 3.1 4.7 - - - -
86A HIS* 2.8 64.7 + - + +
88A ALA* 4.1 8.8 - - + +
118A GLY 4.3 0.6 - - - -
119A THR* 1.3 71.9 - - - +
121A ARG* 1.3 59.6 + - - +
163A TYR* 4.6 3.4 - - + -
164A SER 3.2 9.6 - - - +
165A LEU* 4.0 5.2 - - - +
1196A ACT 4.1 0.2 - - - +
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Residues in contact with ARG 121 (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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62A ARG* 5.3 2.8 - - - +
67A ASP* 4.6 3.4 + - - -
84A GLN 4.4 9.6 - - - +
85A GLY* 4.4 8.1 - - - -
86A HIS* 5.1 1.1 - - - -
119A THR* 4.1 2.8 + - + +
120A ALA* 1.3 75.1 - - - +
122A VAL* 1.3 69.1 + - - +
123A LEU* 3.6 21.0 - - + +
127A ASP* 5.5 2.6 + - - -
163A TYR* 3.3 7.0 - - - -
164A SER* 2.8 63.7 + - - +
166A SER* 4.4 15.4 - - - -
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Residues in contact with VAL 122 (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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84A GLN 4.8 8.4 + - - +
86A HIS* 5.5 0.6 - - - -
121A ARG* 1.3 79.3 - - - +
123A LEU* 1.3 69.5 + - - +
124A ALA* 5.5 0.5 - - - +
160A THR 5.6 0.2 - - - +
161A SER* 4.5 10.1 - - - +
162A VAL 3.3 26.9 - - - +
163A TYR* 3.9 19.8 - - + -
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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