Contacts of the strand formed by residues 118 - 125 (chain A) in PDB entry 1XRG
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.3 20.8 - - + +
48A ILE* 4.0 8.1 - - + -
51A GLN* 3.9 17.9 - - + +
52A ALA* 3.9 34.1 - - + +
55A VAL* 3.8 8.6 - - + +
78A VAL* 4.3 1.3 - - + -
79A PHE 3.4 11.9 - - - +
80A ILE* 3.9 6.3 - - + -
89A VAL* 3.8 38.8 - - + -
112A LEU* 3.4 5.5 - - - +
116A VAL* 3.5 6.1 - - - +
117A LEU* 1.3 82.3 - - - +
119A GLU* 1.3 62.7 + - - +
120A ILE* 4.0 26.0 - - + -
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Residues in contact with GLU 119 (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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32A GLY* 3.6 22.4 - - - +
33A GLN 3.2 13.9 - - - +
34A ILE* 3.9 8.1 - - + -
55A VAL* 4.8 0.2 - - - -
79A PHE* 2.8 42.1 + - + +
112A LEU* 3.6 14.2 - - + +
113A PRO* 3.2 18.8 - - - +
118A ILE* 1.3 76.0 - - - +
120A ILE* 1.3 66.5 + - - +
105C SER* 3.5 15.4 - - - -
106C CYS 3.0 40.6 + - - +
107C VAL* 4.2 7.6 - - - +
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Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLY* 4.0 1.3 - - - -
33A GLN* 2.8 42.6 + - - +
55A VAL* 3.7 22.0 - - + +
56A LEU* 4.2 20.9 - - + -
59A LEU* 4.3 18.8 - - + +
76A THR* 4.3 13.0 - - + -
77A THR 3.3 7.2 - - - +
78A VAL* 3.9 26.5 - - + -
89A VAL* 5.3 1.3 - - + -
93A TYR* 4.4 10.1 - - + -
118A ILE* 4.0 19.7 - - + -
119A GLU* 1.3 79.5 - - - +
121A GLU* 1.3 72.8 + - - +
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Residues in contact with GLU 121 (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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30A THR* 3.7 11.9 - - - +
31A SER 4.0 1.6 - - - +
32A GLY* 3.9 6.9 - - - +
59A LEU* 4.9 0.2 - - - -
76A THR* 3.1 9.1 - - - -
77A THR* 3.0 53.5 + - - +
79A PHE* 4.3 4.4 - - + -
119A GLU 4.4 0.2 - - - -
120A ILE* 1.3 76.4 - - - +
122A ALA* 1.3 62.7 + - - +
123A VAL* 6.3 0.7 - - + -
504A UNX 3.7 9.7 - - - -
505A UNX 2.8 21.8 - - - -
507A UNX 3.7 0.3 - - - -
75C LYS* 3.0 21.8 + - - -
105C SER* 2.4 41.2 + - - +
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Residues in contact with ALA 122 (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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28A VAL 3.7 1.6 - - - +
29A TYR* 3.9 2.3 - - - -
30A THR* 3.1 37.6 + - + +
59A LEU* 3.8 29.6 - - + -
63A LEU* 4.7 2.0 - - + -
73A VAL* 4.0 23.1 - - + -
75A LYS 3.2 8.7 - - - +
76A THR* 4.3 2.0 - - + +
121A GLU* 1.3 77.3 - - - +
123A VAL* 1.3 64.3 + - - +
124A ALA 4.1 0.2 - - - -
75C LYS* 6.1 0.2 - - - -
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Residues in contact with VAL 123 (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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27A PHE* 4.3 12.6 - - + -
28A VAL 3.4 8.1 - - - +
29A TYR* 3.9 31.9 - - + -
73A VAL* 3.7 2.8 - - - +
74A VAL* 2.9 28.4 + - + -
75A LYS* 2.7 32.0 + - + +
121A GLU* 6.1 2.7 - - + +
122A ALA* 1.3 76.8 - - - +
124A ALA* 1.3 61.5 + - - +
29B TYR* 3.7 34.5 - - + +
75C LYS* 6.5 0.9 - - - -
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Residues in contact with ALA 124 (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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27A PHE* 3.5 8.8 - - - -
28A VAL* 2.8 33.8 + - + +
63A LEU* 3.6 24.0 - - + -
68A SER* 3.5 18.8 - - - +
72A LYS 3.4 11.2 - - - +
73A VAL* 3.9 8.7 - - + +
74A VAL* 4.2 1.6 - - - +
123A VAL* 1.3 75.0 - - - +
125A ILE* 1.3 65.7 - - - +
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Residues in contact with ILE 125 (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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26A SER 3.1 11.0 - - - +
27A PHE* 4.2 19.3 - - + -
28A VAL* 4.5 1.1 - - - -
68A SER* 2.7 27.2 + - - -
72A LYS* 2.9 33.7 + - + +
74A VAL* 4.1 9.9 - - + -
124A ALA* 1.3 78.1 - - - +
126A LYS* 1.3 61.0 + - - +
-3B LYS 5.6 0.2 - - - -
-2B ALA* 3.6 26.0 - - + +
1B MSE 4.1 25.6 - - + -
2B TYR* 4.4 0.4 - - - -
3B ILE* 3.7 24.0 - - + -
24B THR* 3.7 22.2 - - - +
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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