Contacts of the strand formed by residues 112 - 120 (chain B) in PDB entry 4P5K
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 LEU 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO* 3.6 2.6 - - - +
102B SER* 3.0 46.9 + - - +
110B HIS* 4.0 30.1 - - + -
111B ASN* 1.3 78.2 + - - +
113B LEU* 1.3 63.0 + - - +
114B VAL* 4.9 4.5 - - + -
141B VAL* 6.5 0.7 - - + -
158B MET* 3.6 36.8 - - + -
159B LEU 3.4 10.8 - - - +
160B GLU* 4.6 14.1 - - + +
161B MET* 4.0 8.8 - - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.3 4.9 - - + -
100B SER 3.6 11.7 - - - +
101B PRO* 4.2 9.6 - - + -
112B LEU* 1.3 72.7 - - - +
114B VAL* 1.3 63.5 + - - +
115B CYS 4.1 0.2 - - - -
129B TRP* 3.4 37.3 - - + -
157B VAL 3.9 0.7 - - - +
158B MET* 2.9 6.1 - - - +
159B LEU* 2.8 41.8 + - + +
161B MET* 3.7 32.1 - - + -
169B TYR* 4.2 10.8 - - + -
186B TRP* 4.0 42.8 - - + -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 3.3 8.7 - - - +
99B VAL* 3.4 2.9 - - - -
100B SER* 2.9 40.6 + - - +
101B PRO 4.4 1.1 - - - +
102B SER* 3.8 24.7 - - - +
112B LEU* 4.9 4.0 - - + -
113B LEU* 1.3 78.4 - - - +
115B CYS* 1.3 59.9 + - - +
116B HIS* 4.4 8.3 - - + +
129B TRP* 4.4 2.2 - - - -
156B LEU* 3.9 28.5 - - + -
157B VAL 4.0 1.6 - - - -
158B MET* 4.4 20.4 - - + +
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Residues in contact with CYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 5.3 2.7 - - - -
98B ASN 3.7 3.4 - - - -
99B VAL* 4.1 11.0 - - + -
114B VAL* 1.3 71.2 - - - +
116B HIS* 1.3 61.6 + - - +
117B VAL* 3.7 14.3 + - - +
127B VAL* 4.3 7.0 - - + -
129B TRP* 3.5 13.9 - - + +
155B ILE 3.7 0.7 - - - +
156B LEU* 3.4 4.2 - - - -
157B VAL* 2.8 41.1 + - - +
171B CYS* 2.0 50.5 - - - -
173B VAL* 4.8 1.6 - - - -
184B VAL* 4.9 4.5 - - - -
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Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 5.3 6.1 + - - +
95A GLU 4.6 2.8 + - - -
96A PRO* 3.7 40.1 - - + +
96B ARG 3.8 0.7 - - - +
97B VAL* 3.5 1.9 - - - +
98B ASN* 2.8 53.0 + - - +
114B VAL* 3.5 6.5 + - + -
115B CYS* 1.3 70.5 - - - +
117B VAL* 1.3 64.6 + - - +
118B THR* 3.9 13.4 - - + +
154B GLN* 3.2 27.7 + - + -
155B ILE 3.8 3.2 + - - -
156B LEU* 3.4 39.9 - - + +
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Residues in contact with VAL 117 (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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95B PRO* 3.5 31.2 - - + -
96B ARG 3.2 6.7 - - - +
97B VAL* 4.0 9.6 - - + -
115B CYS* 4.0 16.2 - - - +
116B HIS* 1.3 76.7 + - - +
118B THR* 1.3 61.3 + - - +
120B PHE* 3.6 12.0 - - + -
125B ILE* 4.0 8.3 - - + -
127B VAL* 4.0 22.9 - - + -
154B GLN* 3.2 6.1 - - - +
155B ILE* 2.8 41.8 + - + +
173B VAL* 4.1 14.1 - - + -
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Residues in contact with THR 118 (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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94A LYS 3.4 22.9 - - - +
95A GLU* 3.2 20.6 + - - -
96A PRO* 3.8 18.8 - - + +
95B PRO* 3.5 2.8 - - - +
96B ARG* 2.6 53.2 + - - +
116B HIS* 3.9 19.0 + - + +
117B VAL* 1.3 79.1 - - - +
119B ASP* 1.3 67.0 + - - +
120B PHE* 3.5 3.4 - - - -
153B PHE 3.9 0.4 - - - -
154B GLN* 3.9 14.6 - - + -
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Residues in contact with ASP 119 (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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94A LYS* 3.4 30.1 + - - +
95A GLU* 2.5 30.2 - - - +
93B VAL* 3.5 15.6 - - + +
94B GLN 3.1 13.9 - - - +
96B ARG* 4.1 19.0 - - + -
118B THR* 1.3 76.5 - - - +
120B PHE* 1.3 60.1 + - - +
148B ASN* 4.0 5.6 + - - +
152B THR* 3.7 19.2 + - + -
153B PHE 3.1 11.1 + - - -
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Residues in contact with PHE 120 (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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93B VAL* 3.2 13.9 - - - +
95B PRO* 3.7 20.9 - - + -
117B VAL* 3.6 39.0 - - + -
118B THR 4.1 2.5 - - - -
119B ASP* 1.3 78.5 - - - +
121B TYR* 1.3 62.8 + - - +
122B PRO 3.5 21.1 - - - -
123B GLY 3.8 12.6 - - - -
125B ILE* 3.7 24.0 - - + -
145B LEU* 3.8 13.0 - - + -
152B THR* 3.5 2.8 - - - -
153B PHE* 2.9 60.0 + - + +
154B GLN* 3.8 5.2 - - - -
155B ILE* 4.1 3.8 - - + -
175B HIS* 3.9 10.8 - + + -
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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