Contacts of the strand formed by residues 102 - 108 (chain A) in PDB entry 1KYZ
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 VAL 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.2 30.7 - - + -
95A ARG 3.3 3.8 - - - +
96A THR* 3.5 23.8 - - + +
100A GLY 4.2 1.8 + - - +
101A LYS* 1.3 79.6 - - - +
103A GLN* 1.3 64.2 + - - +
104A ARG* 4.3 20.2 + - - +
302E VAL* 3.4 26.0 - - + -
333E LYS* 6.3 0.9 - - - +
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Residues in contact with GLN 103 (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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58A SER* 3.5 26.8 + - - -
59A PRO* 4.8 3.3 - - + +
60A ILE* 3.9 23.0 - - - +
78A ASP* 6.0 0.2 - - - -
93A SER 3.8 0.2 - - - +
94A VAL* 3.6 1.0 - - - -
95A ARG* 2.6 71.5 + - + +
97A GLN* 2.9 35.7 + - + +
101A LYS 3.7 3.3 + - - +
102A VAL* 1.3 76.1 - - - +
104A ARG* 1.3 73.9 + - - +
105A LEU 4.0 0.3 + - - -
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Residues in contact with ARG 104 (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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58A SER* 3.7 2.9 - - - -
59A PRO* 3.3 26.1 - - - +
78A ASP* 2.6 40.1 + - - +
82A ARG* 3.8 28.3 - - - +
92A CYS* 3.7 18.4 - - - -
93A SER 3.4 3.4 - - - -
94A VAL* 4.1 14.6 - - + -
102A VAL* 4.3 23.9 + - - +
103A GLN* 1.3 77.0 - - - +
105A LEU* 1.3 63.0 + - - +
106A TYR* 3.4 23.2 + - + +
302E VAL* 3.2 27.1 + - - +
304E PRO* 4.3 12.6 - - - -
331E THR* 6.3 1.2 - - - +
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Residues in contact with LEU 105 (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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56A GLN* 3.8 28.2 - - + +
57A ILE* 3.7 1.8 - - - -
58A SER* 3.5 29.8 - - - +
92A CYS* 3.2 5.9 - - - -
93A SER* 2.7 48.9 + - - +
95A ARG* 3.7 53.8 - - + +
103A GLN* 4.3 0.9 - - - +
104A ARG* 1.3 74.6 - - - +
106A TYR* 1.3 62.2 + - - +
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 3.9 18.7 - - + +
56A GLN* 3.1 4.6 - - - -
57A ILE* 2.8 42.1 + - - +
59A PRO* 3.8 9.4 - - + -
62A ILE* 4.7 1.3 - - + -
78A ASP* 2.8 38.0 + - - -
81A LEU* 3.5 49.8 - - + -
82A ARG* 3.3 7.1 + - - +
85A ALA* 3.9 13.0 - - + -
90A LEU* 4.1 16.6 - - + -
91A THR 3.4 11.9 - - - +
92A CYS* 3.9 13.5 - - + -
104A ARG* 3.4 33.4 - - + -
105A LEU* 1.3 75.0 - - - +
107A GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 107 (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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48A ILE* 4.0 4.9 - - - -
55A ALA 3.2 19.7 - - - -
56A GLN* 3.9 3.4 - - - +
90A LEU* 3.1 12.1 - - - +
91A THR* 2.7 43.0 + - - -
106A TYR* 1.3 75.0 - - - +
108A LEU* 1.3 60.9 + - - -
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Residues in contact with LEU 108 (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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45A LEU* 3.9 20.6 - - + +
48A ILE* 3.6 27.9 - - + +
49A ALA* 4.0 13.5 - - + -
55A ALA 4.4 1.8 + - - -
89A ILE 4.3 0.7 - - - -
90A LEU* 3.8 19.3 - - + -
91A THR* 3.7 9.9 - - - +
107A GLY* 1.3 72.5 - - - -
109A ALA* 1.3 67.9 + - - +
112A ALA* 3.8 11.7 - - + -
113A LYS* 3.8 31.0 - - + +
116A 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