Contacts of the strand formed by residues 115 - 121 (chain K) in PDB entry 3IT8
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 115 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111K GLU* 4.2 2.0 - - - -
112K THR* 2.8 33.1 + - - +
113K ALA 3.3 1.0 + - - -
114K ASN* 1.3 81.2 - - - +
116K PRO* 1.3 79.0 - - - +
117K LEU* 3.4 1.0 + - - +
243K TYR* 5.0 0.4 - - - -
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Residues in contact with PRO 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K GLU* 3.9 8.7 - - + -
115K GLY* 1.3 84.2 - - - +
117K LEU* 1.3 62.8 + - - +
130K MET* 3.6 31.0 - - + -
131K THR* 3.7 19.8 + - - +
242K ASN* 4.0 27.6 - - + +
243K TYR* 3.1 35.6 - - + +
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Residues in contact with LEU 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80K ILE* 4.0 21.1 - - + -
86K THR* 5.8 5.4 - - + -
110K VAL* 2.9 28.5 + - + +
111K GLU* 4.4 3.6 - - - -
112K THR* 4.1 17.3 - - - +
115K GLY 3.4 2.6 + - - +
116K PRO* 1.3 76.4 - - - +
118K ALA* 1.3 59.8 + - - +
129K LYS* 4.0 2.9 - - - -
130K MET* 3.1 25.0 + - - +
131K THR* 4.4 2.4 + - - -
134K GLY 4.2 11.1 - - - +
135K PHE* 3.8 27.3 - - + +
136K PRO* 4.2 10.5 - - + -
141K LEU* 4.0 24.7 - - + -
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Residues in contact with ALA 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K TYR* 3.3 1.0 - - - -
110K VAL* 2.7 33.4 + - + +
117K LEU* 1.3 83.0 - - + +
119K ARG* 1.3 59.1 + - - +
127K PHE* 3.7 24.9 - - + -
128K THR 3.5 6.5 - - - +
130K MET* 3.2 7.6 - - - +
135K PHE* 3.6 30.3 - - + -
141K LEU* 4.2 8.7 - - + -
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Residues in contact with ARG 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K GLY 4.4 4.7 - - - +
109K TYR* 3.8 6.5 - - + -
118K ALA* 1.3 74.5 - - - +
120K TYR* 1.3 67.6 + - - +
121K HIS* 3.5 34.3 + - + +
127K PHE* 3.3 3.0 - - - -
128K THR* 2.7 40.8 + - - +
129K LYS 4.4 4.2 + - - -
130K MET* 3.4 37.5 - - + +
242K ASN 2.9 26.3 + - - -
243K TYR* 3.7 0.4 - - - +
244K GLU* 3.3 28.5 + - - +
247K GLU* 2.8 42.1 + - - +
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Residues in contact with TYR 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K GLY 2.8 22.0 + - - +
119K ARG* 1.3 75.2 - - - +
121K HIS* 1.3 72.8 + - - +
122K THR* 4.1 7.6 - - - -
125K LYS* 3.5 25.5 - - - +
126K ARG* 3.7 28.5 - - - -
127K PHE* 3.7 28.3 - + + -
148K TRP* 4.1 12.8 - + - -
151K VAL* 5.2 1.3 - - + -
152K LYS* 3.8 21.9 - - + +
155K LEU* 4.0 13.0 - - + -
156K GLY* 3.4 33.5 - - - -
159K GLU* 3.1 36.5 - - - +
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Residues in contact with HIS 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119K ARG* 3.5 32.5 + - - -
120K TYR* 1.3 76.3 + - - +
122K THR* 1.3 60.3 + - - +
123K GLY 4.4 1.6 - - - +
124K ASP* 3.7 25.6 - - + +
125K LYS* 2.8 32.2 + - - -
126K ARG 3.0 13.7 + - - +
128K THR* 3.0 37.8 + - + +
159K GLU* 5.0 0.2 - - - -
244K GLU* 4.7 8.1 - - - -
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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