Contacts of the strand formed by residues 123 - 131 (chain B) in PDB entry 3K5N
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 PRO 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B GLY 3.8 7.2 - - - +
6B PHE* 3.7 13.2 - - + -
120B ILE* 3.9 5.7 - - - +
121B THR* 3.1 17.5 + - + +
122B SER* 1.3 93.2 - - - +
124B VAL* 1.3 74.9 + - - +
142B PRO* 4.0 1.0 - - - +
143B HIS* 3.6 33.4 + - + +
146B TYR 3.9 11.0 - - - +
147B ARG* 3.2 26.0 - - - +
357B THR* 3.9 9.6 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ALA* 3.1 5.9 - - - +
5B GLY* 2.8 38.1 + - - +
7B ILE* 4.1 17.7 - - + -
25B LEU* 4.2 16.2 - - + -
120B ILE* 3.2 34.1 - - + -
122B SER 4.1 3.4 - - - +
123B PRO* 1.3 87.2 - - - +
125B TRP* 1.3 67.9 + - - +
126B VAL* 5.0 1.6 - - + +
140B LEU* 4.1 15.3 - - + -
141B LYS 3.3 13.5 - - - +
143B HIS* 3.6 12.8 + - - +
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Residues in contact with TRP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ALA* 3.8 29.8 - - + -
3B GLN* 3.2 10.5 - - - +
4B ALA* 3.6 25.1 - - + -
124B VAL* 1.3 76.5 - - - +
126B VAL* 1.3 62.2 + - - +
127B GLU* 4.2 0.4 - - + -
140B LEU* 3.3 6.4 - - - +
141B LYS* 2.9 50.6 + - + +
142B PRO 3.5 23.8 + - - -
143B HIS* 3.5 37.0 + + + +
144B PRO* 4.6 4.6 - - + +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 4.1 1.9 - - - +
2B ALA* 4.0 0.5 - - - -
3B GLN* 2.5 53.8 + - + +
4B ALA 5.0 1.8 - - - -
5B GLY 5.0 0.7 - - - +
25B LEU* 3.5 26.2 - - + -
32B LEU* 4.9 2.0 - - + -
34B VAL* 3.9 20.6 - - + -
124B VAL* 5.0 1.8 - - + -
125B TRP* 1.3 76.1 - - - +
127B GLU* 1.3 69.5 + - - +
128B GLY 4.4 0.2 + - - -
135B ILE* 4.1 16.0 - - + +
138B ALA* 4.2 2.9 - - + -
139B ARG 4.0 2.9 - - - -
140B LEU* 3.7 26.5 - - + -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 4.8 14.3 + - + -
1B MET 4.1 8.7 - - - +
2B ALA* 3.7 28.9 - - + +
125B TRP* 5.2 0.6 - - + +
126B VAL* 1.3 82.8 - - - +
128B GLY* 1.3 58.8 + - - +
138B ALA* 3.5 1.2 - - - +
139B ARG* 3.0 63.1 + - + +
141B LYS* 4.0 25.3 + - + +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 3.8 20.1 + - - +
1B MET 4.6 2.4 + - - +
127B GLU* 1.3 77.6 - - - +
129B ASP* 1.3 66.5 + - - +
130B MET 3.8 1.7 + - - -
135B ILE* 3.8 18.7 - - - +
137B ASN 3.2 16.8 - - - -
139B ARG* 3.8 9.1 - - - +
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 4.7 7.5 + - - +
128B GLY* 1.3 78.0 - - - +
130B MET* 1.3 67.3 + - - +
131B HIS* 5.9 0.7 - - + -
135B ILE* 4.5 1.1 - - - -
136B VAL* 3.1 37.9 + - + +
137B ASN* 4.2 16.4 - - - +
139B ARG* 4.9 5.0 + - - -
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Residues in contact with MET 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A SER* 3.7 34.8 + - - +
191A LEU 3.7 22.2 - - - +
192A ASP* 4.5 18.8 - - - +
0B HIS 5.0 4.5 - - - +
32B LEU* 4.9 6.5 - - + -
128B GLY 3.8 2.6 + - - -
129B ASP* 1.3 76.5 - - - +
131B HIS* 1.3 63.5 + - - +
133B GLY* 2.6 55.2 - - - +
134B THR 3.2 4.3 - - - +
135B ILE* 4.2 22.6 - - + +
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A SER* 3.6 22.6 + - - -
190A SER* 5.5 1.6 - - - -
129B ASP* 3.6 0.9 + - + -
130B MET* 1.3 78.7 - - - +
132B ASN* 1.3 93.3 + - + +
134B THR* 2.8 24.3 + - - +
136B VAL* 3.8 29.4 - - + +
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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