Contacts of the strand formed by residues 154 - 161 (chain A) in PDB entry 1KIT
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 HIS 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A THR 3.5 2.3 - - - +
99A GLU* 3.2 10.7 - - - +
100A MET 3.0 27.3 + - - +
131A LEU* 4.1 8.9 - - + +
145A ALA* 4.2 8.0 - - + +
149A ALA* 2.8 39.6 + - - +
150A ALA 5.5 0.2 - - - -
152A GLU* 3.7 13.5 + - - +
153A TYR* 1.3 87.4 + - - +
155A LYS* 1.3 62.2 + - - +
156A PHE* 3.6 10.8 - - + -
172A PHE* 3.2 38.4 - + + -
173A ASP* 3.0 26.4 + - - -
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Residues in contact with LYS 155 (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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95A ARG* 5.5 2.6 - - - +
97A THR* 3.2 36.1 + - + +
98A THR 3.7 4.5 - - - +
99A GLU* 4.7 15.9 - - + +
154A HIS* 1.3 74.6 - - - +
156A PHE* 1.3 61.6 - - - +
157A GLU* 3.9 22.3 + - + +
171A TYR 3.8 0.4 - - - +
172A PHE* 3.5 9.2 - - - -
173A ASP* 3.0 43.8 + - - +
174A GLY 5.3 0.9 - - - +
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Residues in contact with PHE 156 (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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96A MET 3.5 1.2 - - - +
97A THR* 3.4 4.2 - - - +
98A THR* 2.8 51.4 + - + +
100A MET* 4.2 27.6 - - + -
102A VAL* 6.0 0.7 - - + -
110A ASN* 5.9 0.4 - - - +
123A ILE* 3.7 24.9 - - + -
131A LEU* 4.0 12.1 - - + -
144A LEU* 3.3 29.2 - - + -
154A HIS* 3.6 30.5 - - + -
155A LYS* 1.3 74.6 - - - +
157A GLU* 1.3 62.2 + - - +
170A PHE* 3.6 26.2 - + + -
171A TYR 3.6 2.0 - - - -
172A PHE* 3.5 21.3 - + - -
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Residues in contact with GLU 157 (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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95A ARG* 3.5 21.8 + - - +
96A MET 3.2 6.3 - - - +
97A THR* 3.7 12.2 + - - +
155A LYS* 3.9 23.3 + - + -
156A PHE* 1.3 81.7 - - - +
158A LEU* 1.3 60.3 + - - +
159A VAL* 4.7 4.5 - - + -
169A SER 3.5 1.2 - - - +
170A PHE* 3.1 12.1 - - - -
171A TYR* 2.7 56.8 + - + +
174A GLY* 4.5 8.4 + - - +
771A LEU* 2.8 37.6 - - + +
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Residues in contact with LEU 158 (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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94A TRP* 3.8 29.3 - - + -
95A ARG* 3.2 4.9 - - - +
96A MET* 2.7 47.5 + - + +
110A ASN 5.0 4.9 - - - +
111A TYR* 5.0 4.9 - - - -
119A VAL* 4.1 36.8 - - + +
121A PRO* 4.5 15.0 - - + -
157A GLU* 1.3 73.8 - - - +
159A VAL* 1.3 61.9 + - - +
160A PHE 4.3 0.7 - - - -
168A ALA* 4.5 4.0 - - + -
169A SER 3.3 15.7 - - - +
170A PHE* 4.0 20.9 - - + -
181A ILE* 4.5 6.7 - - + -
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Residues in contact with VAL 159 (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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94A TRP* 4.1 6.1 - - - +
95A ARG* 4.4 16.2 - - + -
157A GLU* 4.7 1.8 - - + -
158A LEU* 1.3 81.0 - - - +
160A PHE* 1.3 60.7 + - - +
161A LEU* 4.1 7.4 + - + +
168A ALA* 2.8 12.5 - - - -
169A SER* 2.6 52.6 + - - +
171A TYR* 3.7 21.1 - - + -
767A MET* 6.5 0.2 - - + -
768A PRO* 4.7 11.4 - - + -
771A LEU* 4.3 13.7 - - + -
772A LEU* 4.2 23.6 - - + -
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Residues in contact with PHE 160 (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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89A ALA 4.9 3.6 - - - -
90A SER* 5.6 5.4 - - - -
93A GLY* 3.6 19.9 - - - -
94A TRP* 3.0 67.6 + + + +
117A GLN* 4.9 9.0 - - - -
119A VAL* 4.4 12.1 - - + -
158A LEU 4.3 0.4 - - - -
159A VAL* 1.3 73.7 - - - +
161A LEU* 1.3 74.3 + - - +
162A PRO* 3.8 7.6 - - + +
166A PRO* 3.6 31.9 - - + -
167A SER* 3.1 22.9 - - - -
168A ALA* 3.4 13.9 - - + -
181A ILE 5.4 0.7 - - - -
183A PRO* 4.5 13.9 - - + -
214A GLN* 5.8 0.3 - - - +
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Residues in contact with LEU 161 (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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159A VAL* 4.1 9.2 + - + +
160A PHE* 1.3 79.0 - - - +
162A PRO* 1.3 74.5 - - + +
163A GLY* 3.5 1.4 + - - -
166A PRO* 3.8 4.7 - - - +
167A SER* 3.1 32.2 + - - +
168A ALA* 6.2 0.2 - - - -
169A SER* 5.9 1.1 - - - +
731A ILE* 3.7 20.6 - - + -
732A GLN* 3.9 18.4 - - + +
733A LEU* 4.6 2.2 - - + -
767A MET* 4.2 19.1 - - + -
772A LEU* 4.1 20.0 - - + -
775A LYS* 3.6 34.5 - - + -
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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