Contacts of the strand formed by residues 116 - 121 (chain A) in PDB entry 6H1D
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 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.9 12.3 - - + +
50A LEU* 4.0 22.7 - - + -
112A LEU* 4.1 17.5 - - + +
114A GLU 3.8 0.2 - - - -
115A LYS* 1.3 77.9 - - - +
117A ASP* 1.3 60.1 + - - +
118A LEU 3.2 30.3 - - - +
119A LEU* 3.9 16.2 - - + -
162A LEU* 3.0 39.0 + - + +
163A LEU* 3.4 9.1 - - + +
164A SER* 2.9 23.7 + - - -
167A GLY* 4.0 0.3 - - - -
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Residues in contact with ASP 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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43A LEU* 5.6 0.3 - - - +
46A VAL* 4.0 11.9 - - + +
47A GLU* 2.8 32.7 + - - +
48A ILE 2.9 17.4 + - - +
115A LYS 4.0 4.9 - - - +
116A VAL* 1.3 73.1 - - - +
118A LEU* 1.3 60.7 + - - +
164A SER* 2.6 32.0 + - - -
166A ARG* 3.0 41.2 + - - +
167A GLY* 3.5 3.9 - - - -
168A LEU* 3.0 26.0 + - - +
49B LYS* 6.0 0.2 - - - -
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Residues in contact with LEU 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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36A LEU* 4.5 1.3 - - + -
43A LEU* 3.8 16.4 - - + -
46A VAL* 3.9 17.7 - - + -
48A ILE 3.3 2.6 + - - -
49A CYS* 3.3 22.5 - - - -
50A LEU 2.9 26.3 + - - +
63A LEU* 3.9 19.7 - - + -
67A ILE* 3.8 24.7 - - + -
116A VAL* 3.2 4.3 - - - +
117A ASP* 1.3 80.3 - - - +
119A LEU* 1.3 62.3 + - - +
120A VAL* 4.0 10.8 - - + -
168A LEU* 3.4 5.8 - - + +
170A TYR* 3.6 36.3 - - + -
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Residues in contact with LEU 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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50A LEU* 3.3 39.9 - - + +
52A VAL* 4.1 5.6 - - + -
116A VAL* 3.9 4.9 - - + +
118A LEU* 1.3 74.6 - - - +
120A VAL* 1.3 65.2 + - - +
155A PHE* 3.8 31.2 - - + -
159A VAL* 4.0 17.9 - - + -
162A LEU* 4.2 14.1 - - + -
163A LEU* 3.9 14.1 - - + -
168A LEU 2.8 12.9 + - - +
169A PHE* 3.2 25.1 - - + -
170A TYR 2.9 26.0 + - - -
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Residues in contact with VAL 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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32A LEU* 3.6 35.9 - - + -
36A LEU* 4.4 4.9 - - + -
49A CYS* 5.3 0.7 - - - -
50A LEU 3.0 9.2 + - - +
51A GLU* 3.4 14.7 - - + +
52A VAL* 2.8 28.9 + - - +
59A VAL* 4.1 12.8 - - + -
63A LEU* 4.1 15.5 - - + -
118A LEU* 4.0 24.9 - - + -
119A LEU* 1.3 82.5 - - - +
121A PHE* 1.3 66.3 + - - +
169A PHE* 4.6 0.9 - - - -
170A TYR* 3.5 11.4 - - + +
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Residues in contact with PHE 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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52A VAL* 3.1 34.5 - - + -
53A GLY* 4.5 0.4 - - - -
104A LEU* 4.0 28.0 - - + -
120A VAL* 1.3 77.9 - - - +
122A ASN* 1.3 63.3 + - - +
123A PRO* 3.1 42.9 - - + +
124A PRO* 4.1 11.4 - - + -
151A VAL* 4.3 5.8 - - + -
152A MET* 4.6 8.5 - - - -
155A PHE* 3.6 30.3 - + + -
169A PHE* 4.0 15.0 - - + -
170A TYR 3.0 8.6 + - - -
171A LEU* 3.4 13.6 - - + +
172A VAL* 3.3 16.2 + - - -
301A SAH 4.4 12.1 - + - -
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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