Contacts of the strand formed by residues 94 - 104 (chain A) in PDB entry 3NJ0
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 SER 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL 3.8 0.2 - - - +
86A THR* 3.5 3.0 - - - -
87A VAL* 2.9 40.6 + - - +
89A SER* 5.6 1.6 + - - -
92A PRO 3.3 7.2 + - - -
93A ALA* 1.3 76.3 - - - +
95A THR* 1.3 68.5 + - - +
119A HIS* 5.1 13.0 + - - -
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Residues in contact with THR 95 (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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84A GLU* 4.1 28.1 + - + +
85A VAL 3.3 5.4 - - - -
86A THR* 3.9 21.3 - - + +
94A SER* 1.3 79.3 - - - +
96A SER* 1.3 60.4 - - - +
97A THR* 4.4 2.6 - - - +
117A GLY* 3.6 20.0 - - - -
119A HIS* 3.6 6.3 + - - -
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG 3.7 0.7 - - - +
84A GLU* 3.7 0.2 - - - -
85A VAL* 2.7 44.1 + - - +
87A VAL* 4.4 15.7 - - - -
95A THR* 1.3 74.7 - - - +
97A THR* 1.3 63.8 + - - +
98A GLU* 3.4 22.2 + - - +
114A VAL* 4.1 3.8 - - - +
116A GLY 3.6 1.3 - - - -
119A HIS* 3.1 31.3 - - - -
300A PYV 4.9 3.7 + - - -
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.2 12.1 - - + -
82A VAL* 4.0 12.1 - - - +
83A ARG 3.3 7.0 - - - +
84A GLU* 3.8 28.7 - - + +
95A THR* 5.6 2.0 - - - +
96A SER* 1.3 78.1 - - - +
98A GLU* 1.3 56.0 + - - +
114A VAL* 3.4 6.4 - - - +
115A VAL* 2.7 38.6 + - - +
116A GLY* 2.9 29.7 + - - +
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Residues in contact with GLU 98 (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 PHE* 3.6 4.6 - - + -
60A PRO* 5.7 0.2 - - - +
64A LYS* 4.7 1.2 + - - -
82A VAL* 3.3 4.5 - - - -
83A ARG* 2.8 71.3 + - + +
85A VAL* 3.7 17.0 - - + +
87A VAL* 6.1 0.2 - - - +
96A SER* 3.4 17.7 + - - +
97A THR* 1.3 80.3 - - - +
99A ARG* 1.3 60.3 + - - +
112A PHE* 3.5 19.4 - - + -
113A ARG 3.3 8.3 - - - +
114A VAL* 4.0 10.8 - - + -
115A VAL* 4.5 0.2 - - - -
300A PYV 3.1 30.2 + - - -
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 3.8 3.6 - - - -
79A VAL* 5.8 2.4 - - - +
80A GLY* 3.7 29.9 + - - +
81A SER 3.3 11.2 - - - +
82A VAL* 4.1 12.3 - - + +
98A GLU* 1.3 73.8 - - - +
100A LEU* 1.3 69.6 + - - +
101A GLU* 2.8 51.0 + - - +
112A PHE* 3.2 5.2 - - - +
113A ARG* 2.9 30.3 + - + +
115A VAL* 3.6 23.3 - - + +
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Residues in contact with LEU 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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55A ARG* 4.0 6.3 - - - +
57A PHE* 3.5 29.9 - - + -
77A GLY 3.4 25.6 - - - +
78A ASP 3.6 17.9 - - - +
79A VAL* 3.6 5.1 - - + +
80A GLY* 2.8 29.8 + - - -
81A SER 2.9 14.1 + - - +
99A ARG* 1.3 73.6 + - - +
101A GLU* 1.3 58.8 + - - +
102A PHE 4.0 0.7 - - - +
103A VAL* 3.7 24.7 - - + -
110A LEU* 3.6 32.1 - - + -
111A SER 3.5 17.3 - - - +
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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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79A VAL* 3.6 15.0 - - - +
99A ARG* 2.8 60.7 + - - +
100A LEU* 1.3 73.5 - - - +
102A PHE* 1.3 63.1 - - + +
111A SER* 2.9 22.3 + - - +
112A PHE* 4.2 1.3 - - - -
113A ARG* 3.5 41.0 + - + +
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Residues in contact with PHE 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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25A TYR* 4.3 17.7 - + - -
79A VAL* 4.0 5.5 - - - +
100A LEU* 3.7 1.0 - - - +
101A GLU* 1.3 82.3 - - + +
103A VAL* 1.3 77.4 + - - +
104A ASP* 3.8 33.9 - - + -
109A VAL* 3.9 25.8 - - + -
110A LEU* 3.4 0.9 - - - -
111A SER* 2.8 42.8 + - - +
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Residues in contact with VAL 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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51A TRP* 4.1 3.1 - - + -
55A ARG* 3.3 35.4 - - - +
79A VAL* 3.7 16.5 - - + +
100A LEU* 3.7 35.0 - - + -
102A PHE* 1.3 89.8 - - - +
104A ASP* 1.3 64.9 + - - +
105A ASP* 3.6 20.9 - - - +
109A VAL 3.3 8.1 - - - +
110A LEU* 4.3 6.3 - - + -
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Residues in contact with ASP 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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25A TYR* 3.7 8.7 + - - -
51A TRP* 4.2 0.2 - - - -
102A PHE* 3.8 22.7 - - + -
103A VAL* 1.3 74.3 - - - +
105A ASP* 1.3 58.4 + - - +
106A ASP* 3.1 9.7 + - - +
107A HIS* 3.0 42.2 + - - -
108A ARG* 2.8 25.8 + - - -
109A VAL* 2.8 23.8 + - + +
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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