Contacts of the strand formed by residues 123 - 128 (chain B) in PDB entry 4K8T
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 ARG 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ALA* 3.1 35.7 + - - +
32B ALA 4.2 2.4 + - - +
115B ILE* 3.7 16.6 - - + -
116B PHE 3.5 4.0 - - - +
117B VAL* 4.4 1.3 - - + -
122B GLU* 1.3 85.6 + - - +
124B SER* 1.3 63.6 + - - +
125B MSE 3.3 40.4 - - + +
156B TYR* 4.3 6.1 + - - -
186B SER 5.3 3.4 + - - -
187B ASP* 5.7 2.0 + - - -
270B ASP* 3.9 6.7 - - - +
271B THR* 3.4 21.4 + - - +
272B THR* 3.1 39.3 - - - +
273B GLY 4.8 0.8 - - - +
401B ADN 4.2 10.9 + - - -
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Residues in contact with SER 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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23B LEU* 3.7 17.5 - - - +
28B ILE* 3.9 23.1 - - - -
29B THR 4.1 3.1 - - - -
30B LYS* 3.3 9.5 - - - +
31B ALA 3.0 22.6 + - - +
32B ALA 3.9 4.0 - - - -
34B ASN* 4.8 0.2 - - - -
116B PHE* 2.9 36.9 + - - +
118B THR* 5.5 0.9 + - - +
122B GLU* 5.1 1.0 + - - +
123B ARG* 1.3 73.8 + - - +
125B MSE 1.3 62.0 + - - +
126B ASN* 3.3 10.1 + - - -
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Residues in contact with MSE 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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32B ALA 2.9 8.2 + - - +
33B MSE 3.6 12.3 - - + +
34B ASN* 2.7 38.8 + - - -
113B SER* 3.5 10.5 - - - +
114B MSE 3.6 3.4 - - - -
115B ILE* 3.9 12.3 - - + +
123B ARG* 3.3 40.6 - - + +
124B SER* 1.3 73.1 - - - +
126B ASN* 1.3 61.2 + - - +
127B THR* 4.1 3.8 - - - +
156B TYR* 3.3 26.5 - - - +
401B ADN 3.4 57.7 - - + +
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Residues in contact with ASN 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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28B ILE* 3.6 26.0 - - - +
34B ASN* 3.3 22.3 - - - +
36B ILE* 3.7 17.4 - - + +
40B ARG* 4.8 1.7 + - - -
44B LEU* 3.8 29.0 - - + +
112B ARG 3.9 0.9 - - - +
113B SER* 3.3 2.7 + - - -
114B MSE 2.8 49.2 + - + +
116B PHE* 3.4 16.0 - - - -
124B SER 3.3 10.3 + - - -
125B MSE 1.3 79.0 + - - +
127B THR* 1.3 59.9 + - - +
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Residues in contact with THR 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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11B ILE* 3.9 19.7 - - + -
33B MSE 3.7 16.2 - - - +
34B ASN 2.8 9.7 + - - -
35B LEU* 3.6 8.4 - - - +
36B ILE* 3.0 27.1 + - - +
112B ARG 3.6 9.6 - - - +
113B SER* 2.8 16.3 + - - -
126B ASN* 1.3 70.7 + - - +
128B TYR* 1.3 63.3 + - - +
129B LEU* 3.8 13.8 + - + -
401B ADN 2.7 39.9 + - - +
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Residues in contact with TYR 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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36B ILE* 3.5 26.9 - - + +
37B ASP* 4.2 1.8 - - - -
38B ALA* 3.8 27.8 - - + +
41B ALA* 4.3 8.1 - - + -
107B PHE* 4.7 6.6 - - - -
108B PRO* 4.1 5.7 - - - +
109B PRO* 3.8 20.1 - - + +
111B ALA* 3.3 3.3 - - - +
112B ARG* 2.9 51.4 + - - +
114B MSE 6.1 0.2 - - + -
126B ASN 4.0 0.6 + - - -
127B THR* 1.3 71.3 - - - +
129B LEU* 1.3 64.7 + - - +
130B GLY* 3.5 26.4 - - - -
403B DMS 3.6 41.8 - - + +
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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