Contacts of the strand formed by residues 98 - 112 (chain A) in PDB entry 4HVY
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 LEU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A PHE* 5.1 1.8 - - + -
58A LEU* 4.0 23.6 - - + -
89A GLN 4.7 1.0 - - - +
92A VAL* 3.5 19.5 + - + +
93A LYS* 3.5 21.8 + - - +
96A ALA* 3.2 10.2 - - + +
97A GLY* 1.3 80.0 - - - +
99A HIS* 1.3 69.6 + - - +
100A CYS* 4.1 0.3 + - - -
124A PRO* 4.2 22.0 - - + -
126A GLY 3.5 13.7 - - - +
127A GLY 4.2 2.2 - - - +
128A ILE 3.8 3.4 - - - +
129A LEU* 3.6 32.5 - - + +
144A TRP* 4.3 7.4 - - + -
202A MG 4.1 19.3 - - - -
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Residues in contact with HIS 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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89A GLN 6.1 0.2 - - - -
93A LYS* 5.2 12.5 - - + +
97A GLY 4.6 2.9 + - - -
98A LEU* 1.3 79.9 - - - +
100A CYS* 1.3 62.7 + - - +
124A PRO* 3.5 5.0 - - - +
125A THR* 2.8 31.5 + - - +
126A GLY* 2.9 13.5 + - - +
127A GLY* 3.7 26.9 + - - -
207A NA 2.9 21.3 - - - -
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Residues in contact with CYS 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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50A PHE* 3.6 21.1 - - + -
88A LEU* 4.5 7.4 - - - -
89A GLN* 3.1 44.3 + - - +
92A VAL* 3.8 33.0 - - + -
99A HIS* 1.3 78.3 - - - +
101A GLU* 1.3 70.3 + - - +
122A ALA* 4.5 8.1 - - + -
123A ARG 3.2 14.4 - - - +
125A THR* 3.5 5.0 + - - -
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Residues in contact with GLU 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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85A VAL* 5.2 1.0 - - - +
89A GLN* 3.5 15.3 + - - -
100A CYS* 1.3 82.8 - - - +
102A PRO* 1.3 83.8 - - + +
122A ALA* 3.4 4.3 - - - -
123A ARG* 2.9 33.7 + - + +
125A THR* 3.8 22.0 + - + +
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Residues in contact with PRO 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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85A VAL* 3.8 33.4 - - + -
88A LEU* 3.9 14.5 - - + -
89A GLN* 4.7 2.0 - - - +
101A GLU* 1.3 101.7 - - + +
103A GLU* 1.3 61.6 + - - +
104A THR 4.8 1.8 - - - +
120A PHE* 3.8 28.0 - - + -
121A LEU 3.7 5.6 - - - +
122A ALA* 4.3 0.7 - - - -
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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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101A GLU 3.6 1.4 + - - +
102A PRO* 1.3 74.7 - - - +
104A THR* 1.3 62.6 + - + +
121A LEU* 2.7 32.0 + - + +
122A ALA 4.7 0.7 - - - +
123A ARG* 3.5 18.9 - - + +
169A TYR* 4.1 13.7 + - + +
170A ARG* 3.0 40.5 + - - -
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Residues in contact with THR 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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102A PRO* 3.7 0.6 - - - -
103A GLU* 1.3 79.8 - - - +
105A LEU* 1.3 70.3 + - - +
106A LEU* 3.8 17.0 - - + -
120A PHE* 3.4 10.6 - - - -
121A LEU* 2.9 44.9 + - + +
169A TYR* 3.8 40.0 + - + -
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Residues in contact with LEU 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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104A THR* 1.3 83.3 + - - +
106A LEU* 1.3 61.1 + - - +
107A SER* 3.6 15.7 - - - +
108A VAL* 3.6 21.8 - - + -
118A PHE* 4.0 16.2 - - + -
119A VAL 3.5 24.0 - - - +
120A PHE* 3.9 32.0 - - + -
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Residues in contact with LEU 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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49A VAL* 4.3 13.7 - - + -
104A THR* 3.5 14.7 + - + -
105A LEU* 1.3 74.3 - - - +
107A SER* 1.3 60.7 + - - +
119A VAL* 2.8 17.5 + - + +
120A PHE 4.3 2.9 - - - -
121A LEU* 3.8 32.3 - - + +
162A LEU 4.5 2.9 - - - +
165A LEU* 3.6 29.4 - - + +
166A ALA* 3.8 27.6 - - + +
169A TYR* 3.6 34.3 - - + -
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Residues in contact with SER 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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105A LEU* 3.4 5.4 - - - +
106A LEU* 1.3 83.3 - - - +
108A VAL* 1.3 73.0 + - - +
109A GLU* 3.7 18.8 + - - +
117A ARG 4.5 0.2 - - - -
119A VAL* 2.9 42.9 + - - +
162A LEU* 5.1 3.1 - - - -
165A LEU* 3.8 17.3 - - - -
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Residues in contact with VAL 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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105A LEU* 3.6 26.9 - - + -
107A SER* 1.3 83.2 + - - +
109A GLU* 1.3 64.4 + - - +
116A VAL* 3.6 26.9 - - + -
117A ARG 3.4 4.0 - - - +
118A PHE* 3.7 20.6 - - + -
201A GOL 3.5 31.4 + - - +
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Residues in contact with GLU 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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107A SER* 3.7 19.2 + - - +
108A VAL* 1.3 73.8 - - - +
110A GLU* 1.3 60.3 + - - +
111A ARG* 3.1 43.9 + - + +
116A VAL* 3.3 6.6 - - - +
117A ARG* 2.9 59.7 + - + +
119A VAL* 4.8 1.3 - - + -
161A HIS* 5.1 5.5 - - - -
162A LEU* 4.0 20.4 - - - +
201A GOL 4.1 3.1 - - - -
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Residues in contact with GLU 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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109A GLU* 1.3 70.4 - - - +
111A ARG* 1.3 65.3 + - - +
112A GLY* 3.2 24.7 + - - +
113A PRO* 4.2 12.5 - - - +
115A TRP 3.7 3.8 - - - +
116A VAL* 4.7 7.4 - - + +
201A GOL 3.7 35.4 + - - +
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Residues in contact with ARG 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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109A GLU* 3.1 45.9 + - + +
110A GLU* 1.3 72.9 - - - +
112A GLY* 1.3 56.6 + - - +
115A TRP* 2.9 57.1 + - + +
117A ARG* 3.7 23.0 - - + +
158A ASP* 3.5 35.8 + - - +
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Residues in contact with GLY 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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110A GLU* 3.2 17.6 - - - +
111A ARG* 1.3 77.7 - - - +
113A PRO* 1.3 77.8 - - - +
114A SER 3.0 4.2 + - - -
115A TRP* 3.2 24.7 + - - +
116A VAL* 5.1 0.3 - - - +
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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