Contacts of the strand formed by residues 113 - 122 (chain A) in PDB entry 1NQY
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 PHE 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PRO* 3.8 21.1 - - + -
8A LEU* 3.6 44.0 - - + -
11A ILE* 4.0 18.6 - - + -
19A TRP* 4.0 6.8 - - + -
33A TYR 4.2 0.2 - - - +
34A ARG* 3.3 63.7 - - + -
35A ARG 4.7 0.4 - - - -
36A ALA* 4.1 11.2 - - + -
72A SER* 4.0 15.7 - - - -
108A PHE* 3.1 8.0 - - - +
109A THR* 3.1 43.3 + - + +
111A VAL* 4.9 0.9 - - + -
112A GLY* 1.3 73.5 - - - +
114A HIS* 1.3 65.6 + - - +
115A VAL* 4.9 0.4 - - + -
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Residues in contact with HIS 114 (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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33A TYR* 4.9 15.0 - - - -
34A ARG 2.8 11.1 + - - +
35A ARG* 3.5 13.3 - - + -
36A ALA* 2.8 28.5 + - - +
106A ASP* 3.7 27.6 + - + +
107A VAL 3.6 2.5 - - - -
108A PHE* 3.7 40.3 - + + +
112A GLY* 6.0 0.4 - - - -
113A PHE* 1.3 76.1 - - - +
115A VAL* 1.3 62.3 + - - +
116A THR* 5.4 0.4 - - - +
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Residues in contact with VAL 115 (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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8A LEU* 3.8 24.5 - - + -
19A TRP* 3.7 25.8 - - + -
36A ALA* 3.4 4.7 - - + +
37A ALA* 4.2 7.6 - - - +
38A VAL* 3.8 38.1 - - + -
106A ASP* 3.3 4.6 - - - -
107A VAL* 2.8 44.8 + - + -
113A PHE* 4.9 0.2 - - + -
114A HIS* 1.3 78.5 - - - +
116A THR* 1.3 63.0 + - - +
117A PRO* 3.2 5.5 - - + +
180A MET* 3.9 12.1 - - + -
184A VAL* 5.6 0.4 - - + -
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Residues in contact with THR 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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35A ARG* 5.4 2.6 + - - -
36A ALA 2.9 13.5 + - - -
37A ALA* 3.3 4.7 - - - +
38A VAL 3.2 18.1 + - - -
79A PRO* 3.8 35.5 - - + +
103A GLU* 3.9 29.2 - - + +
104A LEU 4.8 0.2 - - - +
106A ASP* 3.0 26.5 + - - +
114A HIS 5.4 0.7 + - - -
115A VAL* 1.3 73.2 - - - +
117A PRO* 1.3 62.5 - - + +
118A VAL* 3.1 10.4 + - + +
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Residues in contact with PRO 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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38A VAL* 3.7 15.3 - - + +
40A VAL* 4.0 7.2 - - + -
103A GLU* 3.0 6.3 - - - +
104A LEU* 2.9 59.0 + - + +
105A ASP 3.5 16.6 - - - +
106A ASP* 4.1 0.4 - - - -
107A VAL* 4.5 5.2 - - + +
115A VAL* 3.2 14.4 - - + +
116A THR* 1.3 82.3 - - - +
118A VAL* 1.3 60.5 + - - +
119A LEU 3.6 0.3 + - - -
184A VAL* 3.6 31.9 - - + -
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Residues in contact with VAL 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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37A ALA* 4.3 0.7 - - + -
38A VAL 2.9 12.7 + - - +
39A LEU* 3.6 7.6 - - + +
40A VAL* 2.8 26.2 + - - -
79A PRO* 3.9 24.2 - - + +
80A THR* 4.0 22.0 - - + +
83A ALA* 3.7 24.2 - - + -
100A LEU* 4.2 17.0 - - + -
102A GLY 4.0 4.7 - - - +
103A GLU* 4.1 6.7 - - - +
116A THR* 3.7 15.7 - - + +
117A PRO* 1.3 71.4 - - - +
119A LEU* 1.3 70.1 + - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.0 0.9 - - - -
40A VAL* 3.5 19.7 - - + -
42A LEU* 3.9 12.8 - - + -
100A LEU* 3.6 10.6 - - - +
101A LEU* 3.0 37.0 + - + +
102A GLY 2.7 26.2 + - - +
103A GLU 4.1 2.9 - - - +
104A LEU* 3.4 41.5 - - + +
117A PRO 3.6 0.8 + - - +
118A VAL* 1.3 74.7 - - - +
120A GLY* 1.3 58.6 + - - +
188A LEU* 3.6 29.6 - - + -
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Residues in contact with GLY 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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39A LEU* 4.9 1.1 - - - +
40A VAL 3.1 8.4 + - - +
41A ALA* 3.4 5.2 - - - -
42A LEU* 2.9 29.7 + - - +
98A VAL* 3.8 18.4 - - - -
99A THR 3.0 12.6 - - - -
101A LEU* 3.8 5.8 - - - +
118A VAL 3.9 0.4 + - - -
119A LEU* 1.3 77.4 - - - +
121A ARG* 1.3 60.8 + - - -
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Residues in contact with ARG 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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42A LEU* 3.2 34.6 - - - +
43A THR 3.2 20.8 + - - -
44A ARG* 3.8 47.4 + - + +
45A GLU 5.3 0.4 + - - +
48A PRO* 4.9 8.9 - - - +
97A ALA 3.6 1.4 - - - +
98A VAL* 3.5 3.3 - - - -
99A THR* 2.7 45.7 + - - +
101A LEU* 3.7 31.3 - - + +
120A GLY* 1.3 74.4 - - - +
122A ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ALA* 4.2 24.9 - - + +
42A LEU 3.0 12.5 + - - +
43A THR* 3.2 9.1 - - + +
44A ARG* 2.7 36.6 + - - +
51A LEU* 5.4 2.5 - - + -
93A LEU* 4.4 14.4 - - + -
97A ALA 3.7 16.6 - - - +
98A VAL* 3.9 20.2 - - + -
121A ARG* 1.3 78.6 - - - +
123A ALA* 1.3 67.7 + - - +
126A ALA* 4.2 11.9 - - + -
127A LEU* 3.6 32.8 - - + -
130A LEU* 5.8 0.2 - - + -
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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