Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 3P9K
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 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL* 3.5 26.0 - - + -
92A GLU 3.0 14.1 - - - +
93A GLU* 3.6 26.9 - - + -
98A ARG* 1.3 81.8 - - - +
100A SER* 1.3 61.6 + - - +
101A ARG* 3.6 25.8 + - - +
298B PRO 3.7 20.2 - - - +
299B VAL* 3.4 23.1 - - - +
300B ASN* 3.8 14.4 - - + +
301B PRO* 4.3 7.6 - - + -
328B TYR* 3.8 21.4 + - + +
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Residues in contact with SER 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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90A LEU 3.8 0.5 - - - +
91A VAL* 3.5 2.6 - - - -
92A GLU* 2.8 47.3 + - - +
94A GLY* 5.3 5.4 + - - -
98A ARG 3.9 1.5 + - - -
99A LEU* 1.3 74.8 - - - +
101A ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 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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54A THR* 4.0 4.3 - - - +
55A PRO* 3.2 24.7 - - - +
75A ASP* 2.7 36.0 + - - +
79A ARG* 3.1 41.9 - - - +
89A CYS* 4.0 9.0 - - - -
90A LEU 3.3 5.2 - - - +
91A VAL* 3.6 23.3 - - + -
99A LEU* 3.6 29.4 + - - +
100A SER* 1.3 78.0 - - - +
102A SER* 1.3 62.7 + - - +
103A TYR* 3.1 28.1 + - + +
328B TYR* 2.7 28.2 + - - -
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Residues in contact with SER 102 (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 SER* 3.5 18.2 - - - -
53A LEU 3.1 18.4 - - - -
54A THR* 4.5 8.3 - - - -
89A CYS* 3.4 4.3 - - - -
90A LEU* 3.0 50.6 + - - +
101A ARG* 1.3 73.9 - - - +
103A TYR* 1.3 66.9 + - - +
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Residues in contact with TYR 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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45A LEU* 3.6 18.9 - - + +
51A LYS 4.2 0.3 - - - +
52A SER* 3.0 5.6 - - - -
53A LEU 2.6 42.7 + - - +
55A PRO* 3.7 17.0 - - + -
75A ASP* 2.5 37.8 + - - -
78A LEU* 3.5 57.9 - - + -
79A ARG* 3.5 9.5 + - - -
82A ALA* 4.2 0.2 - - + -
87A VAL* 4.0 5.4 - - + -
88A THR 3.3 15.0 - - - +
89A CYS* 3.9 16.4 - - + +
101A ARG* 3.1 32.3 + - + -
102A SER* 1.3 78.4 - - - +
104A GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 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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45A LEU* 3.8 9.0 - - - +
50A GLY 5.0 3.4 - - - -
51A LYS 4.2 10.1 - - - -
52A SER* 3.9 7.4 + - - -
87A VAL* 3.3 10.6 - - - +
88A THR* 2.7 47.4 + - - -
103A TYR* 1.3 75.2 - - - +
105A ALA* 1.3 56.6 + - - -
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Residues in contact with ALA 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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45A LEU* 3.8 32.6 + - + +
46A VAL* 4.0 20.2 - - + +
49A GLY 4.5 11.2 + - - +
50A GLY* 5.5 2.8 + - - -
88A THR* 3.5 10.9 - - - +
104A GLY* 1.3 71.9 - - - -
106A ALA* 1.3 62.1 + - - +
109A CYS* 4.1 10.3 - - + -
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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