Contacts of the strand formed by residues 111 - 122 (chain a) in PDB entry 4N3E
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 GLY 111 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12a SER 3.5 13.2 - - - -
13a PRO* 3.8 3.1 - - - -
14a ILE 3.6 9.6 - - - -
15a ALA* 3.8 3.1 - - - -
16a PRO* 3.6 4.9 - - - +
107a ALA* 3.4 5.5 - - - -
108a VAL 2.6 43.7 + - - -
109a GLY 3.1 1.5 + - - +
110a GLY* 1.3 73.8 - - - +
112a SER* 1.3 58.8 + - - -
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Residues in contact with SER 112 (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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11a GLU* 3.4 8.1 - - - +
12a SER* 3.0 37.4 + - - +
14a ILE 2.5 25.3 + - - -
16a PRO* 3.7 23.6 - - - +
19a LEU* 4.2 9.1 - - - +
105a LEU* 4.7 3.1 - - - -
106a GLU 3.4 12.3 - - - -
108a VAL* 4.1 6.8 + - - +
111a GLY* 1.3 73.1 - - - -
113a LYS* 1.3 68.9 + - - +
201a 2AN 5.6 0.7 - - - -
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Residues in contact with LYS 113 (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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9a GLU* 5.6 5.4 - - - +
10a GLU 3.2 6.3 - - - +
11a GLU* 3.8 35.1 + - + +
104a LYS 4.8 0.4 - - - -
105a LEU* 3.3 9.9 - - - +
106a GLU* 3.1 52.4 + - + +
108a VAL* 4.0 29.2 - - + +
112a SER* 1.3 75.5 - - - +
114a GLY* 1.3 61.0 + - - +
201a 2AN 4.7 2.2 - - - -
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Residues in contact with GLY 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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9a GLU* 3.4 9.7 - - - +
10a GLU 2.7 34.9 + - - +
104a LYS 3.9 4.5 - - - -
105a LEU* 4.0 5.4 - - - -
113a LYS* 1.3 76.9 - - - +
115a LYS* 1.3 62.5 + - - +
116a ILE* 4.1 3.6 - - - -
201a 2AN 3.9 22.2 - - - -
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Residues in contact with LYS 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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7a VAL* 4.4 19.0 - - + +
8a LYS 3.5 13.5 - - - +
9a GLU* 3.7 24.2 - - + +
102a GLU 3.6 3.3 - - - +
103a VAL* 3.7 0.9 - - - -
104a LYS* 3.1 42.3 + - + +
114a GLY* 1.3 74.8 - - - +
116a ILE* 1.3 60.7 + - - +
117a THR* 4.3 3.1 - - - +
83b LYS* 4.8 13.7 - - - +
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Residues in contact with ILE 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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6a ILE 4.0 0.5 - - - +
7a VAL* 3.7 2.6 - - - +
8a LYS* 2.8 47.4 + - + +
9a GLU 5.1 0.9 - - - +
10a GLU* 5.1 2.9 - - + -
101a TYR* 5.2 1.8 - - + -
102a GLU 3.2 10.1 - - - +
103a VAL* 4.2 13.2 - - + -
114a GLY* 4.3 3.8 - - - +
115a LYS* 1.3 84.3 - - - +
117a THR* 1.3 62.5 + - - +
118a VAL* 4.0 22.0 - - + -
201a 2AN 3.1 79.6 - - + +
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Residues in contact with THR 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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5a THR* 4.0 15.0 - - + -
6a ILE 3.3 3.8 - - - -
7a VAL* 3.5 19.5 - - + +
100a VAL 3.6 1.4 - - - +
101a TYR* 3.4 5.0 - - - -
102a GLU* 2.9 51.0 + - + +
115a LYS* 5.6 4.5 + - - +
116a ILE* 1.3 70.9 - - - +
118a VAL* 1.3 64.8 + - - +
119a THR* 3.6 20.4 - - - +
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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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4a TYR 3.6 0.9 - - - +
5a THR* 3.2 4.7 - - - +
6a ILE* 2.7 51.9 + - + +
8a LYS* 3.7 15.7 - - - +
99a VAL* 3.6 24.0 - - + -
100a VAL 3.6 1.8 - - - +
101a TYR* 3.8 19.1 - - + -
116a ILE* 4.0 11.0 - - + -
117a THR* 1.3 76.4 - - - +
119a THR* 1.3 64.4 + - - +
120a TYR* 3.9 4.5 - - + -
137a GLU* 3.1 38.1 - - - +
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Residues in contact with THR 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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3a ALA* 3.4 28.0 - - + -
4a TYR 3.2 3.6 - - - -
5a THR* 3.4 17.6 + - - +
99a VAL* 3.3 5.5 - - - -
100a VAL* 3.0 38.7 + - - -
117a THR* 3.6 15.8 - - - +
118a VAL* 1.3 76.1 + - - +
120a TYR* 1.3 61.4 + - - +
121a HIS* 3.5 19.4 - - + +
5b THR* 4.4 10.5 + - + +
7b VAL* 6.1 0.7 - - + -
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Residues in contact with TYR 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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3a ALA* 3.0 7.2 - - - +
4a TYR* 2.6 50.5 + - + +
6a ILE* 3.8 9.0 - - + -
96a ILE* 4.4 6.3 - - + -
98a LYS 3.9 1.1 - - - -
99a VAL* 3.4 28.8 - - + +
101a TYR* 5.2 1.7 + - - -
118a VAL* 3.9 6.0 - - + +
119a THR* 1.3 75.3 - - - +
121a HIS* 1.3 60.1 + - - +
122a PRO* 3.4 4.2 - - - +
128a VAL* 4.1 10.3 - - + +
132a GLU* 3.5 36.9 + - + -
133a VAL* 3.6 41.5 - - + -
136a GLY* 3.7 9.5 - - - -
137a GLU* 2.5 31.0 + - - -
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Residues in contact with HIS 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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3a ALA* 3.8 15.8 - - + +
96a ILE* 3.6 5.2 - - - +
97a GLU* 2.7 37.8 + - + +
98a LYS* 2.8 55.4 + - + +
100a VAL* 3.6 17.3 - - + +
119a THR* 3.5 30.3 - - + +
120a TYR* 1.3 71.1 - - - +
122a PRO* 1.4 62.2 - - + +
5b THR 5.5 1.6 - - - -
7b VAL* 4.9 20.6 - - + +
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Residues in contact with PRO 122 (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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1a MET 4.3 15.8 + - - +
2a ALA 3.3 24.5 - - - +
3a ALA* 4.0 2.7 - - + -
95a ASN 3.6 7.0 - - - +
96a ILE* 4.5 1.1 - - - -
97a GLU* 3.8 5.9 - - - +
120a TYR 3.4 9.9 - - - +
121a HIS* 1.4 89.7 - - + +
123a LYS* 1.3 63.2 + - - +
124a PRO* 3.9 2.3 - - - +
126a CYS 3.1 29.2 - - - +
127a THR* 4.2 1.1 - - - +
128a VAL* 2.8 30.2 - - + -
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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