Contacts of the strand formed by residues 97 - 101 (chain A) in PDB entry 1K7E
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 ILE 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.9 2.2 - - - -
48A LEU* 3.6 15.9 - - + -
50A LEU* 3.8 25.6 - - + -
85A LEU* 4.1 14.6 - - + +
88A ILE* 4.1 23.8 - - + -
89A ARG* 3.4 38.8 - - + +
95A ILE* 3.7 12.1 - - + +
96A PRO* 1.3 81.4 - - - +
98A GLY* 1.4 62.7 + - - +
99A LEU* 4.7 0.2 - - + -
122A GLY 4.6 3.1 - - - +
123A VAL* 3.7 12.4 - - + +
124A ASP* 2.5 43.8 + - - +
125A SER 3.0 3.6 + - - -
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Residues in contact with GLY 98 (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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4A TYR* 3.6 4.0 + - - -
48A LEU 2.8 15.5 + - - -
49A GLU* 3.4 8.7 - - - -
50A LEU* 2.9 25.6 + - - +
97A ILE* 1.4 73.7 - - - +
99A LEU* 1.3 64.0 + - - +
125A SER* 2.8 26.9 - - - -
173A TYR* 5.5 2.0 - - - -
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Residues in contact with LEU 99 (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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25A LEU* 4.5 4.5 - - + -
49A GLU* 5.3 3.1 - - - -
50A LEU* 3.3 18.6 - - + +
52A VAL* 5.0 2.9 - - + -
82A PHE* 4.1 4.0 - - + -
85A LEU* 3.7 46.2 - - + -
97A ILE* 4.7 0.9 - - + -
98A GLY* 1.3 79.6 - - - +
100A LEU* 1.3 56.9 + - - +
101A MET* 3.9 13.9 - - - -
114A PHE* 4.0 15.7 - - + -
118A CYS* 3.7 30.1 - - - -
123A VAL* 4.1 13.0 - - + -
125A SER 3.0 8.5 + - - -
126A VAL* 3.4 10.5 - - + -
127A LEU* 2.7 35.2 + - - +
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Residues in contact with LEU 100 (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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22A PHE* 4.0 20.6 - - + -
49A GLU* 4.3 8.1 - - - +
50A LEU 3.0 7.4 + - - +
51A GLY* 4.2 2.2 - - - -
52A VAL 3.4 22.7 + - - +
60A ASP* 4.7 0.7 - - - +
99A LEU* 1.3 71.7 - - - +
101A MET* 1.3 71.5 + - - +
102A TYR* 4.1 23.2 - - + -
127A LEU* 3.3 29.8 - - + +
129A ALA* 4.3 4.5 - - + -
401A IAG 3.6 54.5 - - + +
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Residues in contact with MET 101 (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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52A VAL* 3.3 45.1 - - + -
78A PRO* 6.0 1.1 - - + -
82A PHE* 5.9 0.2 - - + -
99A LEU* 4.1 13.2 - - + -
100A LEU* 1.3 79.0 - - - +
102A TYR* 1.3 66.8 + - - +
105A LEU* 3.5 34.1 - - + -
106A VAL* 3.8 17.5 - - + -
114A PHE* 3.6 37.2 - - + -
126A VAL* 4.1 11.0 - - + -
127A LEU 2.7 11.7 + - - +
128A VAL* 4.2 4.0 - - + -
129A ALA* 2.8 31.2 + - - +
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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