Contacts of the strand formed by residues 134 - 142 (chain A) in PDB entry 3HFV
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 ALA 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PRO* 3.7 29.8 - - + -
73A LEU 3.3 13.7 + - - +
74A PHE* 3.6 24.5 - - + -
75A SER* 3.3 18.5 + - - -
132A LEU* 3.8 2.5 - - - +
133A ASP* 1.3 81.6 + - - +
135A PHE* 1.3 64.3 + - - +
161A VAL 3.2 6.3 - - - +
162A ARG* 4.4 1.6 - - + -
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Residues in contact with PHE 135 (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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74A PHE* 3.3 9.6 - - - -
75A SER 3.3 13.9 - - - +
77A TYR* 4.3 3.8 - - + -
124A GLN* 4.0 18.6 - - + -
127A LEU* 3.5 46.7 - - + -
128A LEU* 3.8 15.5 - - + -
132A LEU* 3.7 31.0 - - + -
134A ALA* 1.3 82.0 - - - +
136A LEU* 1.3 60.2 + - - +
137A VAL* 3.9 11.7 - - + -
159A GLU* 5.8 0.9 - - + -
160A ALA* 3.3 4.4 - - - -
161A VAL* 3.1 72.8 + - + +
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Residues in contact with LEU 136 (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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57A VAL* 4.3 10.8 - - + -
58A LYS* 4.2 26.7 - - + -
61A PHE* 4.1 30.5 - - + -
74A PHE* 3.6 26.9 - - + -
75A SER 2.9 8.0 + - - +
76A VAL* 4.2 17.0 - - + -
77A TYR* 3.0 26.4 + - - -
135A PHE* 1.3 74.8 - - - +
137A VAL* 1.3 66.8 + - - +
138A VAL* 5.0 0.7 - - + -
158A LEU* 4.3 12.8 - - + -
159A GLU 3.2 5.6 - - - +
160A ALA* 3.6 27.1 - - + -
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Residues in contact with VAL 137 (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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77A TYR* 3.4 11.2 - - + +
80A LEU* 4.1 7.9 - - + -
117A ARG* 5.6 1.6 - - - +
120A THR* 4.2 14.9 - - + +
123A HIS* 3.8 32.3 - - + -
124A GLN* 6.6 0.2 - - + -
127A LEU* 3.4 33.0 - - + -
135A PHE* 3.9 10.3 - - + -
136A LEU* 1.3 77.2 - - - +
138A VAL* 1.3 69.3 + - - +
157A GLN 3.8 0.6 - - - +
158A LEU* 3.2 3.6 - - - -
159A GLU* 2.6 51.9 + - + +
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Residues in contact with VAL 138 (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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43A HIS* 3.4 21.9 + - + -
54A LYS* 3.7 25.4 - - + -
58A LYS* 5.8 0.2 - - + -
76A VAL* 4.7 11.4 - - + -
77A TYR 3.0 8.6 + - - +
78A ASP* 3.2 32.5 - - + -
80A LEU* 5.4 1.2 + - - +
117A ARG* 4.9 0.7 + - - -
136A LEU* 5.0 1.6 - - + -
137A VAL* 1.3 86.1 - - - +
139A GLY* 1.3 60.6 + - - +
157A GLN 3.3 11.2 - - - +
158A LEU* 3.7 25.4 - - + -
280A LEU* 3.9 21.3 - - + -
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Residues in contact with GLY 139 (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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43A HIS* 3.7 9.9 - - - -
117A ARG* 3.2 19.3 - - - -
120A THR* 4.0 5.0 - - - +
138A VAL* 1.3 78.4 - - - +
140A ASP* 1.3 63.7 + - - -
141A VAL* 3.6 2.3 + - - +
156A HIS* 3.2 10.8 - - - -
157A GLN 3.1 30.9 + - - +
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Residues in contact with ASP 140 (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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37A ARG 4.8 1.4 - - - +
39A GLY 4.3 6.4 + - - -
41A ASN* 3.7 19.5 + - - +
43A HIS* 3.7 12.5 - - - -
80A LEU 5.1 0.7 - - - +
82A PRO* 3.8 12.0 - - - +
117A ARG* 2.8 36.6 + - - -
139A GLY* 1.3 66.3 - - - -
141A VAL* 1.3 60.9 + - - +
142A TYR* 2.5 39.5 + - + +
154A ILE* 4.0 5.6 - - + -
155A PHE 3.2 7.9 - - - +
156A HIS* 3.4 21.7 - - - +
297A TRP* 6.1 0.2 - - + -
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Residues in contact with VAL 141 (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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117A ARG* 3.5 11.7 - - + +
118A ALA 3.9 9.0 - - - +
119A HIS* 3.6 7.2 - - - +
120A THR* 3.6 39.7 - - + +
139A GLY 4.1 2.9 - - - +
140A ASP* 1.3 78.7 - - - +
142A TYR* 1.3 69.2 + - - +
153A PRO 3.8 0.2 - - - +
154A ILE* 3.4 4.0 - - - +
155A PHE* 2.6 78.7 + - + +
156A HIS* 4.6 0.2 - - - -
157A GLN* 3.8 12.1 - - + +
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Residues in contact with TYR 142 (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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34A VAL* 4.0 7.9 - - + -
37A ARG 4.1 2.8 + - - -
38A VAL* 3.5 29.0 + - + +
82A PRO* 3.7 17.2 - - + +
106A ASP 4.9 0.5 - - - +
107A ASN* 5.0 0.5 - - - +
108A TYR* 3.8 18.4 + + + -
115A MET* 5.8 0.2 - - - +
116A LEU* 3.7 46.6 - - + +
117A ARG 2.8 12.1 + - - +
118A ALA* 3.4 14.9 - - - +
140A ASP* 2.5 43.1 + - - +
141A VAL* 1.3 78.7 - - - +
143A ARG* 1.3 69.3 - - - +
153A PRO 3.4 4.3 - - - +
154A ILE* 3.4 46.4 - - + +
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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