Contacts of the strand formed by residues 97 - 104 (chain A) in PDB entry 2PXC
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 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PRO* 3.7 37.0 - - + -
75A GLY 3.6 6.7 - - - +
77A VAL* 3.7 18.4 - - + -
91A ALA 3.2 24.7 - - - +
94A MET* 3.1 12.3 + - + +
95A LYS 3.8 0.5 - - - +
96A ASN* 1.3 78.8 - - - +
98A GLN* 1.3 64.0 + - - +
99A GLU 4.0 2.0 - - - +
100A VAL* 3.6 31.0 - - + -
123A ILE* 4.3 3.1 - - + -
265A ARG* 3.0 31.6 + - - +
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Residues in contact with GLN 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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75A GLY* 3.0 17.0 + - - +
95A LYS 5.6 1.1 - - - +
96A ASN 4.1 9.8 - - - +
97A VAL* 1.3 77.7 - - - +
99A GLU* 1.3 63.7 + - + +
123A ILE* 3.4 27.9 - - - +
265A ARG* 5.8 0.2 - - - +
267A VAL* 3.7 33.0 - - + +
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Residues in contact with GLU 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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75A GLY 3.5 2.8 + - - +
76A LYS* 3.4 46.5 + - + +
77A VAL* 2.7 34.3 + - - +
97A VAL* 3.9 1.3 - - - +
98A GLN* 1.3 83.9 - - + +
100A VAL* 1.3 61.7 + - - +
101A ARG* 3.5 29.5 - - - +
123A ILE* 4.2 6.1 - - + +
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Residues in contact with VAL 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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77A VAL* 3.6 10.5 - - + +
79A ASP* 5.6 1.1 - - + -
88A SER* 3.4 40.4 - - - +
91A ALA* 4.5 7.6 - - + -
92A ALA* 3.7 26.5 - - + +
97A VAL* 3.6 22.2 - - + -
99A GLU* 1.3 78.4 + - - +
101A ARG* 1.3 59.7 + - - +
123A ILE* 3.1 19.2 + - + +
124A VAL* 3.5 7.8 - - + -
125A THR* 2.7 34.3 + - - +
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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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76A LYS* 4.8 1.8 - - - -
77A VAL 2.9 12.7 + - - +
78A VAL* 3.2 13.6 - - + +
79A ASP* 2.9 24.0 + - - -
99A GLU* 3.5 19.4 + - - +
100A VAL* 1.3 75.1 - - - +
102A GLY* 1.3 61.4 + - - +
103A TYR* 3.1 51.1 + - + +
125A THR* 3.4 31.2 - - - +
127A LYS* 3.3 34.0 - - - +
135A LYS* 5.3 1.6 - - - +
138A GLU* 4.4 9.8 + - - +
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Residues in contact with GLY 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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79A ASP* 3.3 12.3 - - - -
82A CYS* 3.8 18.8 - - - -
88A SER* 4.3 5.7 + - - -
100A VAL* 4.2 0.6 - - - +
101A ARG* 1.3 73.2 - - - +
103A TYR* 1.3 72.1 + - - -
124A VAL* 6.1 0.2 - - - +
125A THR 3.0 11.5 + - - +
126A MET* 3.6 3.4 - - - +
127A LYS 3.0 23.0 + - - -
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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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78A VAL* 4.1 15.0 - - + -
79A ASP 3.0 7.6 + - - +
80A LEU* 4.1 17.9 - - + -
81A GLY 2.6 32.9 + - - -
82A CYS* 3.0 6.2 + - - -
101A ARG* 3.1 47.5 + - + +
102A GLY* 1.3 79.5 - - - -
104A THR* 1.3 57.6 + - - +
127A LYS* 3.6 20.0 - - + -
130A VAL* 4.2 29.2 - - + -
132A VAL* 4.2 11.8 - - + +
135A LYS* 3.6 24.9 - - + -
138A GLU* 2.9 30.6 + - - -
171A TRP* 4.2 9.0 - + - -
500A SAM 4.9 1.1 - - - -
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Residues in contact with THR 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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82A CYS* 3.7 8.1 - - - -
83A GLY* 3.4 40.4 + - - +
103A TYR* 1.3 76.5 - - - +
105A LYS* 1.3 71.5 + - - +
106A GLY 4.4 1.8 - - - +
111A GLU 3.9 11.8 + - - +
113A PRO* 3.9 19.7 - - + -
127A LYS 3.2 6.3 + - - +
128A SER* 3.4 2.4 - - - +
129A GLY 3.2 16.6 + - - -
130A VAL* 3.2 11.9 + - - +
500A SAM 3.6 28.5 + - - -
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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