Contacts of the strand formed by residues 115 - 127 (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 TRP 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A CYS* 3.5 11.2 - - + -
45A MET* 3.4 34.5 - - + +
110A GLU 3.7 0.3 - - - -
111A ARG* 2.9 71.1 + - + +
112A GLY* 3.2 16.4 + - - +
113A PRO 3.6 0.2 - - - -
114A SER* 1.3 79.4 - - - +
116A VAL* 1.3 70.5 + - - +
117A ARG* 4.8 12.6 - - - +
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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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42A VAL* 4.1 18.6 - - + -
43A CYS 2.9 7.9 + - - +
44A TYR* 3.4 16.8 - - + +
45A MET* 2.8 27.7 + - - +
108A VAL* 3.6 25.4 - - + -
109A GLU 3.3 11.2 - - - +
110A GLU* 5.0 10.5 - - + -
112A GLY 5.1 0.2 - - - +
113A PRO 5.7 2.2 - - - +
115A TRP* 1.3 84.5 - - - +
117A ARG* 1.3 62.3 + - - +
118A PHE* 3.7 16.6 - - + -
201A GOL 4.7 7.6 - - - -
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Residues in contact with ARG 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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45A MET* 3.4 19.1 - - + +
46A VAL 5.0 0.7 - - - -
47A LEU* 4.3 17.2 - - + +
72A TYR* 3.7 12.4 + - - -
107A SER 3.9 0.7 - - - +
108A VAL* 3.4 4.3 - - - +
109A GLU* 2.9 61.9 + - + +
111A ARG* 3.7 28.3 - - + +
115A TRP* 4.8 12.4 - - - +
116A VAL* 1.3 73.4 - - - +
118A PHE* 1.3 68.4 + - - +
119A VAL* 3.7 20.6 - - + +
158A ASP* 2.6 34.3 + - - -
162A LEU* 4.2 11.5 - - - +
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Residues in contact with PHE 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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44A TYR* 3.4 50.3 - + - -
45A MET 2.8 20.2 + - - +
46A VAL* 3.3 4.0 - - - +
47A LEU* 2.9 26.7 + - - +
84A ILE* 4.1 22.9 - - + -
105A LEU* 4.0 14.6 - - + -
107A SER 3.7 2.7 - - - -
108A VAL* 3.7 29.6 - - + -
116A VAL* 3.7 19.3 - - + -
117A ARG* 1.3 75.0 - - - +
119A VAL* 1.3 61.5 + - - +
120A PHE* 3.9 19.1 - + + -
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Residues in contact with VAL 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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47A LEU* 3.5 23.8 - - + -
49A VAL* 3.9 16.4 - - + -
105A LEU* 3.5 3.4 - - - +
106A LEU* 2.8 42.4 + - + -
107A SER* 2.9 27.7 + - - +
109A GLU* 4.8 3.8 - - - -
117A ARG* 3.7 28.9 - - + +
118A PHE* 1.3 73.0 - - - +
120A PHE* 1.3 55.0 + - - +
162A LEU* 4.1 29.8 - - + -
165A LEU* 5.5 0.2 - - + -
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Residues in contact with PHE 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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46A VAL* 3.6 32.1 - - + -
47A LEU 2.9 9.4 + - - +
48A ALA* 3.6 1.7 - - - -
49A VAL* 2.8 32.4 + - - +
84A ILE* 3.9 26.9 - - + -
85A VAL* 4.4 12.3 - - + -
88A LEU* 3.8 23.8 - - + -
102A PRO* 3.8 22.0 - - + -
104A THR 3.4 14.4 - - - +
105A LEU* 3.9 23.8 - - + -
106A LEU* 4.3 3.8 - - - -
118A PHE* 3.9 16.4 - + + -
119A VAL* 1.3 77.4 - - - +
121A LEU* 1.3 61.1 + - - +
122A ALA 4.9 0.2 - - - +
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Residues in contact with LEU 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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49A VAL 3.3 17.7 - - - +
51A LEU 4.5 4.3 - - - +
102A PRO* 3.7 3.3 - - - +
103A GLU* 2.7 52.5 + - + +
104A THR* 2.9 16.8 + - + +
106A LEU* 3.8 19.9 - - + +
120A PHE* 1.3 71.9 - - - +
122A ALA* 1.3 54.4 + - - +
166A ALA* 3.8 24.2 - - + +
169A TYR* 3.7 33.0 - - + -
170A ARG* 3.6 36.3 - - + +
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Residues in contact with ALA 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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48A ALA* 4.6 9.2 - - + -
49A VAL 2.9 12.3 + - - +
50A PHE* 3.3 45.4 - - + -
51A LEU 4.7 0.2 + - - -
88A LEU* 4.7 6.5 - - + -
100A CYS* 4.5 7.2 - - - -
101A GLU 3.4 14.1 - - - +
102A PRO* 4.6 2.7 - - + -
103A GLU* 4.2 1.1 - - - +
120A PHE 4.8 0.7 - - - +
121A LEU* 1.3 75.2 - - - +
123A ARG* 1.3 67.4 + - - +
124A PRO* 4.5 0.2 - - - +
170A ARG* 4.1 7.2 + - - -
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Residues in contact with ARG 123 (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* 3.7 3.6 - - - -
100A CYS* 3.2 2.4 - - - -
101A GLU* 2.9 36.7 + - + +
103A GLU* 3.5 27.3 - - + +
122A ALA* 1.3 76.3 - - - +
124A PRO* 1.3 74.1 - - + +
125A THR* 3.6 4.4 + - + +
170A ARG* 4.0 9.2 - - - +
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Residues in contact with PRO 124 (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 21.5 - - + -
98A LEU* 4.2 18.6 - - + -
99A HIS 3.5 8.1 - - - +
122A ALA 4.5 0.2 - - - +
123A ARG* 1.3 90.7 - - + +
125A THR* 1.3 63.4 + - - +
126A GLY 3.7 3.6 - - - +
144A TRP* 4.1 22.7 - - + -
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Residues in contact with THR 125 (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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99A HIS* 2.8 27.4 + - - +
100A CYS* 3.3 5.4 + - - -
101A GLU* 3.8 28.7 + - + +
123A ARG* 3.8 10.1 - - + +
124A PRO* 1.3 78.7 - - - +
126A GLY* 1.3 58.9 + - - +
207A NA 3.4 16.1 - - - -
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Residues in contact with GLY 126 (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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98A LEU* 3.5 12.3 - - - +
99A HIS* 2.9 28.1 + - - +
124A PRO* 3.7 2.7 - - - +
125A THR* 1.3 79.7 + - - +
127A GLY* 1.3 66.5 + - - +
207A NA 4.5 0.2 - - - -
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Residues in contact with GLY 127 (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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97A GLY 3.6 11.0 - - - -
98A LEU* 4.2 3.8 - - - +
99A HIS* 3.7 23.8 + - - -
126A GLY* 1.3 77.9 - - - +
128A ILE* 1.3 67.1 + - - +
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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