Contacts of the strand formed by residues 77 - 87 (chain A) in PDB entry 4WCX
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 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS* 4.0 8.0 + - - -
73A ILE 2.9 28.3 + - - -
74A TYR* 3.1 32.5 + - - +
75A GLY* 3.3 4.8 - - - -
76A ASN* 1.3 88.1 + - - +
78A ILE* 1.3 72.4 - - - +
79A VAL* 4.2 4.0 - - + +
328A SER* 4.1 5.0 - - - +
376A LEU* 3.3 11.2 - - + +
378A SER* 5.1 3.6 - - - -
402A ILE* 4.7 1.4 - - - +
403A HIS* 3.1 27.7 + - - -
406A CYS* 3.1 53.5 - - - +
407A LEU* 3.7 20.9 - - + +
410A ALA* 4.0 14.8 - - + -
502A SF4 5.3 3.3 - - - -
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Residues in contact with ILE 78 (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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70A LYS* 3.9 5.2 - - - +
77A ARG* 1.3 83.8 - - - +
79A VAL* 1.3 68.3 + - - +
80A ILE* 3.7 6.6 + - + +
323A ILE* 3.6 22.9 - - + -
327A ILE 3.5 24.5 - - - +
328A SER* 3.7 3.6 - - - +
329A GLN 4.5 0.2 - - - -
330A ILE* 3.8 42.2 - - + +
370A LEU* 4.3 13.2 - - + -
375A TYR* 4.0 28.3 - - + -
376A LEU 3.0 8.1 + - - +
377A PRO* 3.5 4.0 - - - +
378A SER 3.0 21.0 + - - -
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Residues in contact with VAL 79 (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 ARG* 5.6 3.6 - - + -
78A ILE* 1.3 74.6 - - - +
80A ILE* 1.3 64.2 + - - +
129A ARG* 3.5 44.4 - - - +
328A SER 3.0 14.7 + - - +
329A GLN* 3.2 16.2 - - + +
330A ILE 2.9 26.5 + - - +
378A SER* 3.4 27.1 - - - +
380A CYS 4.5 3.6 - - - +
502A SF4 4.5 9.2 - - - -
505A ALA* 4.4 5.4 - - + -
506A H2S 4.4 17.3 - - - -
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Residues in contact with ILE 80 (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 ILE 3.9 12.8 - - - +
79A VAL* 1.3 75.9 - - - +
81A PHE* 1.3 64.9 + - - +
127A HIS* 3.8 17.6 + - + -
129A ARG* 3.8 17.8 + - - +
330A ILE* 3.5 27.8 - - + +
332A ALA* 3.9 17.5 - - + -
363A PRO* 5.9 0.4 - - + -
366A ILE* 5.1 0.2 - - + -
367A LEU* 3.9 25.6 - - + -
370A LEU* 4.3 11.0 - - + -
377A PRO* 4.6 1.1 - - + -
378A SER 2.9 18.8 + - - +
379A TYR* 3.6 42.7 - - + +
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Residues in contact with PHE 81 (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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80A ILE* 1.3 74.4 - - - +
82A ALA* 1.3 84.7 + - - +
83A PRO* 4.5 4.7 - - + -
127A HIS* 3.2 12.0 - - - -
129A ARG* 3.4 29.6 - - + +
130A LEU 5.1 0.4 - - - -
131A ALA* 4.3 19.7 - - + -
167A ASN* 6.0 3.1 - - - +
309A ILE* 3.7 33.9 - - + -
310A LEU 5.3 0.4 - - - -
311A SER* 5.7 2.2 - - - -
329A GLN* 3.9 18.6 - - + +
330A ILE* 3.1 19.4 + - - -
331A SER* 3.1 52.3 - - - -
332A ALA 3.2 7.8 + - - -
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Residues in contact with ALA 82 (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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81A PHE* 1.3 83.0 - - - +
83A PRO* 1.3 72.9 - - + +
122A LEU* 3.8 16.6 - - + -
127A HIS* 3.3 31.4 - - + +
129A ARG 3.1 5.1 + - - -
130A LEU* 3.3 9.8 - - + +
131A ALA 3.0 22.3 + - - -
332A ALA 4.3 4.3 - - - +
334A SER* 5.2 0.9 - - - +
341A TYR* 3.9 5.6 - - + +
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Residues in contact with PRO 83 (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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81A PHE* 4.3 5.6 - - + -
82A ALA* 1.3 88.3 - - + +
84A LEU* 1.3 59.9 + - - +
85A TYR* 3.9 28.0 - - + +
122A LEU* 4.9 0.5 - - - +
130A LEU* 5.4 0.2 - - - -
131A ALA* 3.4 12.8 - - + +
133A GLU* 4.4 11.2 - - + +
331A SER* 4.1 9.6 - - - -
334A SER* 3.6 32.1 - - - +
335A CYS 4.3 2.9 - - - +
336A THR* 4.8 4.0 - - + -
341A TYR* 2.7 33.7 + - - +
355A PHE* 6.4 0.4 - - + -
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Residues in contact with LEU 84 (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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83A PRO* 1.3 74.4 - - - +
85A TYR* 1.3 68.5 + - - +
86A VAL* 3.5 23.0 + - + +
110A LEU* 4.7 1.3 - - + -
115A VAL* 4.9 7.0 - - + -
118A GLU* 3.7 33.0 - - + +
119A VAL* 4.4 16.8 - - + -
122A LEU* 4.1 17.0 - - + -
130A LEU* 4.4 11.2 - - + -
131A ALA 2.9 11.9 + - - +
132A VAL* 3.6 6.5 - - + -
133A GLU* 2.9 24.3 + - - -
153A ILE* 4.0 25.6 - - + -
341A TYR* 4.2 8.3 - - + -
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Residues in contact with TYR 85 (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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83A PRO* 3.9 19.2 - - + +
84A LEU* 1.3 77.3 - - - +
86A VAL* 1.3 60.8 + - - +
87A SER 3.8 1.3 - - - +
99A TYR* 4.4 7.2 - + - -
110A LEU* 4.0 7.6 - - - +
133A GLU* 3.5 27.0 - - + +
335A CYS 3.9 7.4 + - - -
336A THR* 3.4 41.9 - - + +
337A GLY 4.1 18.1 + - - +
338A VAL* 3.5 24.8 - - + +
339A GLY 4.1 1.9 + - - -
341A TYR* 5.3 1.2 - - - -
354A GLN* 2.7 35.0 + - + +
355A PHE* 3.7 17.2 - - - -
503A MET* 3.6 26.9 - - + -
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Residues in contact with VAL 86 (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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84A LEU* 3.6 34.1 - - + +
85A TYR* 1.3 78.3 - - - +
87A SER* 1.3 61.3 + - - +
109A LYS* 3.1 2.3 - - - -
110A LEU* 2.8 45.0 + - + +
115A VAL* 5.1 1.1 - - + -
132A VAL* 4.2 7.6 - - + -
133A GLU 3.1 12.1 + - - +
134A ALA* 4.3 2.0 - - + -
145A TYR* 3.4 27.8 + - + +
146A ILE* 4.2 17.5 - - + -
149A VAL* 4.1 18.6 - - + -
338A VAL* 3.6 5.6 - - - +
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Residues in contact with SER 87 (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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85A TYR* 3.8 2.2 - - - +
86A VAL* 1.3 86.6 - - - +
88A ASN* 1.3 59.7 + - - +
89A TYR* 3.6 23.7 + - - +
99A TYR* 5.7 0.2 - - - -
108A LYS 3.5 6.5 - - - -
109A LYS* 3.6 12.3 - - - +
133A GLU 4.0 1.6 + - - +
134A ALA* 3.4 3.4 - - - -
135A GLY 2.9 26.5 + - - -
141A CYS* 3.7 34.7 - - - +
145A TYR* 4.4 0.9 - - - -
338A VAL* 3.8 3.3 - - - +
503A MET* 5.0 1.7 - - - -
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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