Contacts of the strand formed by residues 118 - 129 (chain A) in PDB entry 5V5W
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 ALA 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ALA 3.3 29.5 + - - +
26A GLN* 3.9 5.6 - - - +
27A ALA* 3.9 22.5 - - + +
108A CYS 3.9 0.3 - - - +
109A LYS* 3.3 3.8 - - - +
110A ALA* 2.8 38.3 + - + +
116A VAL 3.6 1.0 + - - +
117A PRO* 1.3 72.4 - - - +
119A ILE* 1.3 61.2 + - - +
120A LYS* 4.3 2.7 - - + -
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Residues in contact with ILE 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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107A TYR* 4.2 22.9 - - + -
108A CYS 3.2 9.4 - - - +
109A LYS* 4.1 28.0 - - + +
117A PRO* 4.0 8.9 + - + +
118A ALA* 1.3 81.4 - - - +
120A LYS* 1.3 79.9 + - - +
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Residues in contact with LYS 120 (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 ALA* 3.2 42.6 + - + +
28A GLN* 4.5 5.8 - - - +
29A ILE* 3.8 22.0 - - + +
43A ILE* 4.6 12.7 + - - +
44A SER* 4.5 23.5 - - - +
107A TYR* 3.2 6.1 - - - +
108A CYS* 2.7 34.0 + - + +
118A ALA* 6.0 2.5 - - - -
119A ILE* 1.3 86.1 - - - +
121A SER* 1.3 61.1 + - - +
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Residues in contact with SER 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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29A ILE* 3.7 6.8 - - - +
44A SER* 5.1 1.4 + - - -
45A GLU 3.9 10.7 - - - +
46A ARG* 4.6 9.2 + - - -
105A ARG* 2.9 29.0 + - - -
106A TYR 3.1 13.2 - - - -
107A TYR* 3.5 24.9 - - - -
120A LYS* 1.3 78.2 - - - +
122A ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 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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29A ILE* 4.1 22.2 - - + -
38A VAL* 5.4 0.7 - - + -
45A GLU* 3.9 35.4 - - + +
46A ARG 3.4 16.2 - - - +
47A VAL 3.9 7.4 - - - +
48A TYR* 4.0 19.7 - - + +
58A LEU* 3.7 33.7 - - + -
72A TRP* 5.0 0.2 - - + -
104A GLY 3.7 0.7 - - - +
105A ARG* 3.5 7.3 - - - +
106A TYR* 2.9 37.8 + - + +
121A SER* 1.3 76.6 - - - +
123A ARG* 1.3 68.0 + - - +
124A VAL* 3.9 4.9 + - + -
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Residues in contact with ARG 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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39A LYS* 4.9 7.3 - - - +
46A ARG 3.0 14.8 + - - +
47A VAL* 3.2 22.8 - - + +
48A TYR 2.7 31.5 + - - -
104A GLY* 3.6 15.3 - - - +
105A ARG* 3.9 22.5 - - + +
122A ILE* 1.3 73.5 - - - +
124A VAL* 1.3 62.9 + - - +
125A ASP* 4.3 24.0 + - - +
301A SO4 2.9 40.6 + - - -
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Residues in contact with VAL 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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48A TYR* 3.3 17.9 - - + +
50A ILE* 4.4 3.6 - - + -
56A LEU* 3.6 31.6 - - + -
58A LEU* 4.5 9.0 - - + -
98A ILE* 4.0 5.8 - - + -
102A GLN 4.4 1.6 - - - +
103A GLY* 3.4 8.5 - - - -
104A GLY* 2.8 36.5 + - - +
106A TYR* 3.6 26.7 - - + -
122A ILE* 4.6 2.5 - - + +
123A ARG* 1.3 79.1 + - - +
125A ASP* 1.3 61.3 + - - +
126A VAL* 3.9 21.8 - - + -
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Residues in contact with ASP 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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47A VAL* 4.4 4.7 - - + -
48A TYR 2.9 9.3 + - - -
49A THR* 3.4 20.6 + - - +
50A ILE 3.0 24.6 + - - +
123A ARG* 4.0 20.1 + - - +
124A VAL* 1.3 72.5 - - - +
126A VAL* 1.3 61.1 + - - +
127A GLN* 3.3 23.6 - - - +
162A ASN* 2.6 34.3 + - - +
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Residues in contact with VAL 126 (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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50A ILE* 3.3 5.8 - - + +
51A ARG 4.4 0.2 - - - -
52A GLU* 3.6 32.3 - - + +
98A ILE* 3.8 26.7 - - + +
99A ALA 3.6 17.5 - - - +
100A ARG* 3.7 27.7 - - + +
103A GLY* 3.9 19.2 - - - +
124A VAL* 3.9 4.8 + - + -
125A ASP* 1.3 73.9 + - - +
127A GLN* 1.3 61.6 + - - +
128A TYR* 3.7 10.4 - - - -
162A ASN* 2.9 20.3 + - - -
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Residues in contact with GLN 127 (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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37A VAL* 6.0 0.8 - - - +
49A THR* 3.5 20.8 - - + +
50A ILE 3.0 8.2 + - - +
51A ARG* 3.6 1.2 - - - +
52A GLU* 2.9 23.4 + - - +
125A ASP* 3.3 23.2 - - - +
126A VAL* 1.3 77.2 - - - +
128A TYR* 1.3 60.7 + - - +
162A ASN* 3.1 15.0 - - - +
163A PRO* 3.5 22.0 - - + +
221A VAL* 3.5 21.3 - - - +
222A CYS* 3.1 27.4 - - - -
224A ILE* 3.6 17.6 - - + +
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Residues in contact with TYR 128 (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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51A ARG* 5.8 0.4 - - - -
52A GLU* 3.5 21.5 - - + +
100A ARG* 3.3 64.5 - - + +
126A VAL 3.7 9.9 - - - -
127A GLN* 1.3 78.8 - - - +
129A LEU* 1.3 64.8 + - - +
130A ASP* 3.9 4.3 - - - +
160A ASN* 3.8 8.1 - - + +
161A SER* 3.2 35.7 + - - -
162A ASN* 2.9 49.0 + - + +
218A VAL* 4.5 1.8 - - - +
224A ILE* 3.6 12.1 - - - +
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Residues in contact with LEU 129 (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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128A TYR* 1.3 76.7 - - - +
130A ASP* 1.3 67.2 + - - +
159A VAL* 3.7 21.1 - - + -
160A ASN 3.9 1.3 - - - -
161A SER* 3.6 20.2 - - - -
165A ALA* 4.2 10.1 - - + -
216A VAL* 3.6 32.8 - - + +
217A SER* 4.0 0.7 - - - -
218A VAL* 4.0 24.7 - - + +
224A ILE* 3.7 17.8 - - + +
225A PRO 3.7 19.7 - - - +
226A ASP* 4.3 1.1 - - - -
227A LYS* 3.2 25.5 + - + +
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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