Contacts of the strand formed by residues 103 - 108 (chain D) in PDB entry 1XPM
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 ARG 103 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C TYR* 3.1 21.7 + - - +
116C PRO* 4.3 13.3 - - - +
119C GLN* 3.4 28.6 + - - +
120C LEU* 4.0 11.7 - - - +
123C ASP* 4.8 1.4 + - - -
175C ALA* 3.7 13.7 - - - +
177C ALA* 3.7 11.6 - - + +
179C THR* 4.6 0.2 - - - -
310C VAL* 4.6 1.1 - - - -
312C GLU* 2.8 35.6 + - - +
72D GLY 3.0 8.3 + - - +
73D MET* 3.2 27.2 - - + +
74D VAL 2.8 27.0 + - - +
102D ALA* 1.3 73.2 - - - +
104D CYS* 1.3 60.4 + - - +
105D PHE* 4.2 9.1 - - + -
124D TYR* 3.5 34.1 - - + +
128D ARG* 5.3 4.9 - - - +
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Residues in contact with CYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLU* 3.4 20.3 - - - +
112C TYR* 4.2 2.5 - - - -
179C THR* 3.5 25.1 + - - +
310C VAL* 3.6 7.8 - - + +
74D VAL* 3.3 11.9 - - - -
87D ALA* 4.5 1.1 - - - +
89D ALA* 3.9 18.6 - - + -
90D VAL* 4.0 10.3 - - + -
93D HIS* 3.5 41.5 - - - -
102D ALA 3.8 2.3 + - - -
103D ARG* 1.3 79.4 - - - +
105D PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C MET* 4.0 19.7 - - + -
108C LYS 3.6 14.6 - - - +
109C GLU* 3.8 7.6 - - + -
112C TYR* 4.7 4.7 - + + -
113C ALA* 5.9 0.4 - - - -
116C PRO* 3.9 25.1 - - + -
120C LEU* 3.7 23.8 - - + -
73D MET* 4.2 7.0 - - - -
74D VAL 3.3 4.2 + - - -
75D ILE* 3.4 33.7 - - + -
76D VAL 3.1 21.8 + - - -
87D ALA* 3.7 9.9 - - - -
89D ALA* 3.5 5.5 - - - +
103D ARG* 4.2 15.9 - - + -
104D CYS* 1.3 84.2 - - - +
106D GLU* 1.3 71.1 + - - +
107D MET* 3.7 23.3 - - + -
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Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C MET* 3.3 5.2 - - - -
108C LYS* 2.8 78.4 + - + +
76D VAL* 3.1 24.2 - - + +
78D THR* 3.5 23.1 - - + +
81D ALA* 3.8 7.5 - - - +
82D VAL 5.6 0.5 + - - -
86D LYS 3.9 0.9 - - - +
87D ALA* 4.1 1.8 - - + -
88D ALA* 2.8 38.9 + - - +
105D PHE* 1.3 79.0 - - - +
107D MET* 1.3 66.2 + - - +
108D LYS* 5.9 2.9 - - + +
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Residues in contact with MET 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C PHE* 4.1 18.8 - - + -
106C GLU 3.3 5.6 - - - +
107C MET* 3.8 16.8 - - + -
120C LEU* 4.5 2.9 - - + -
75D ILE* 3.9 14.6 - - + +
76D VAL 2.9 7.8 + - - +
77D ALA* 3.5 1.6 - - - -
78D THR 3.4 17.2 + - - +
105D PHE* 3.7 26.5 - - + -
106D GLU* 1.3 79.9 - - - +
108D LYS* 1.3 61.1 + - - +
113D ALA* 3.4 27.4 - - + +
116D PRO* 4.0 4.3 - - - +
117D ALA* 3.6 41.1 - - - -
120D LEU* 4.1 17.5 - - + -
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Residues in contact with LYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 3.8 7.5 - - - +
83C ASP 2.6 26.2 + - - +
84C ALA* 3.5 23.6 - - - +
85C ALA* 3.8 16.4 - - - +
86C LYS 3.7 8.0 + - - -
87C ALA* 3.4 9.3 - - - +
105C PHE* 4.4 1.5 - - - +
106C GLU* 2.8 83.9 + - + +
108C LYS* 6.3 3.4 - - + -
78D THR 3.6 17.3 - - - +
79D GLU* 4.7 0.4 - - - -
106D GLU* 5.9 3.4 - - + +
107D MET* 1.3 75.1 - - - +
109D GLU* 1.3 66.9 + - - +
110D ALA 4.6 0.7 - - - +
113D ALA* 4.1 2.2 - - - -
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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