Contacts of the strand formed by residues 134 - 141 (chain A) in PDB entry 5NKS
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 ASP 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A THR 3.6 5.1 + - - +
103A MET* 3.3 30.1 - - + -
104A ILE 3.3 2.8 + - - -
133A CYS* 1.3 83.0 - - - +
135A TYR* 1.3 61.6 + - - +
397A ARG* 4.2 0.7 + - - -
398A LYS* 2.6 32.7 + - - +
408A ASP* 4.2 1.9 - - - +
448A SER* 4.7 1.8 + - - -
449A GLN* 3.6 14.6 + - - +
467A ARG* 2.8 60.6 + - - +
469A VAL* 4.1 7.2 - - + -
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Residues in contact with TYR 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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89A PHE* 3.8 17.7 - + + -
103A MET* 3.9 6.7 - - - +
104A ILE* 3.2 26.5 - - + +
124A ARG* 3.3 15.1 + - - -
127A ALA* 3.3 32.6 - - + +
128A ASP* 2.4 27.6 + - - -
131A ALA* 3.9 18.2 - - + -
133A CYS 4.2 1.6 - - - +
134A ASP* 1.3 77.0 - - - +
136A SER* 1.3 71.1 + - - +
137A LEU* 4.0 13.5 - - + -
466A GLY 4.3 2.5 - - - -
467A ARG 2.9 15.8 + - - +
468A PHE* 3.4 34.7 - + + -
469A VAL* 2.9 26.3 + - - +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A MET* 3.9 6.7 - - - -
104A ILE 3.0 7.4 + - - +
105A LEU* 3.3 19.2 - - - +
106A ASP 2.9 23.3 + - - -
135A TYR* 1.3 79.0 - - - +
137A LEU* 1.3 69.3 + - - +
468A PHE* 3.5 11.7 - - - -
469A VAL 2.6 26.9 + - - -
471A ARG* 2.6 29.1 + - - +
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Residues in contact with LEU 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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89A PHE* 4.7 1.6 - - + -
105A LEU* 5.6 0.4 - - - -
106A ASP* 3.2 20.6 - - + +
108A VAL* 3.9 19.5 - - + -
120A TYR* 3.9 21.5 - - + -
123A TRP* 3.7 33.9 - - + -
124A ARG* 3.8 28.7 - - + +
127A ALA* 5.4 0.4 - - + -
135A TYR* 4.0 17.7 - - + -
136A SER* 1.3 88.1 + - - +
138A HIS* 1.3 62.1 + - - +
161A VAL* 4.1 10.4 - - + +
468A PHE* 4.1 5.6 - - + -
471A ARG* 2.7 27.6 + - - +
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Residues in contact with HIS 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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72A VAL 2.9 23.0 + - - -
105A LEU* 3.3 28.7 - - + +
106A ASP 2.8 6.6 + - - +
107A HIS* 3.4 42.0 - + - +
108A VAL* 2.8 29.3 + - - +
137A LEU* 1.3 74.9 - - - +
139A VAL* 1.3 63.3 + - - +
140A ASP* 4.5 0.4 - - - +
163A SER* 2.7 28.2 + - - +
196A GLN* 3.6 18.0 + - - +
392A PHE* 3.5 34.8 - + - -
471A ARG* 4.3 1.9 + - - -
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Residues in contact with VAL 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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108A VAL* 3.9 25.8 - - + +
116A LEU* 4.0 37.2 - - + +
120A TYR* 4.6 5.2 - - + -
137A LEU 5.1 0.2 - - - +
138A HIS* 1.3 79.0 - - - +
140A ASP* 1.3 66.7 + - - +
141A ILE 3.7 0.4 + - - +
155A LEU* 4.2 14.6 - - + -
161A VAL* 4.1 24.7 - - + -
163A SER 3.2 7.3 + - - -
164A PHE* 3.1 27.9 - - + +
165A LEU 3.0 19.9 + - - -
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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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75A ARG* 2.8 35.1 + - - -
107A HIS* 2.6 30.4 + - - +
108A VAL 2.8 20.9 + - - +
109A PHE* 3.8 14.4 - - + +
110A PRO* 3.3 22.3 - - - +
116A LEU* 3.5 9.0 - - - +
139A VAL* 1.3 75.5 + - - +
141A ILE* 1.3 59.8 + - - +
142A THR 3.5 0.7 + - - -
165A LEU* 3.4 20.3 - - - +
167A PHE* 3.8 17.3 - - + -
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Residues in contact with ILE 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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116A LEU* 4.4 15.9 - - + -
139A VAL 4.4 1.1 - - - +
140A ASP* 1.3 70.7 - - - +
142A THR* 1.3 59.1 + - - +
143A ARG 3.7 24.5 - - - +
144A TRP* 4.7 1.8 - - - +
148A ILE* 5.2 7.9 - - + -
152A LEU* 4.0 27.1 - - + -
164A PHE* 3.9 26.9 - - + -
165A LEU 2.8 18.8 + - - +
166A VAL* 4.4 9.1 - - + -
167A PHE* 3.7 15.5 + - - -
174A CYS 4.5 2.9 - - - +
176A CYS* 5.0 6.1 - - - -
184A ILE* 4.1 37.7 - - + -
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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