Contacts of the strand formed by residues 118 - 127 (chain D) in PDB entry 4QAE
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 HIS 118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D TRP* 3.7 6.6 - - - -
112D SER* 4.1 18.3 + - - -
113D THR* 2.7 26.0 + - - -
114D ASN* 3.0 50.8 + - - +
117D GLN* 1.3 95.8 - - - +
119D ALA* 1.3 63.4 + - - +
120D MET* 5.7 1.4 - - - +
137D LEU* 4.9 3.8 - - + +
138D TYR 3.2 9.9 - - - +
144D LEU* 4.2 6.5 - - + -
148D LEU* 3.8 41.4 - - + +
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Residues in contact with ALA 119 (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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27D PHE* 3.5 26.9 - - + -
31D TRP* 3.9 3.3 - - + -
110D VAL* 5.2 0.2 - - + -
112D SER 3.1 13.2 - - - +
113D THR* 3.5 9.6 - - - +
118D HIS* 1.3 79.3 - - - +
120D MET* 1.3 62.8 + - - +
121D VAL* 4.4 2.5 - - + -
137D LEU* 3.4 9.2 - - - +
138D TYR* 2.7 48.2 + - + +
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Residues in contact with MET 120 (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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110D VAL* 3.8 0.7 - - - +
111D VAL* 2.9 38.6 + - + -
112D SER* 2.8 25.0 + - - +
118D HIS* 5.7 2.0 - - - +
119D ALA* 1.3 77.0 - - - +
121D VAL* 1.3 65.1 - - - +
135D VAL* 4.6 4.7 - - + -
136D THR 3.2 8.7 - - - +
137D LEU* 3.9 14.8 - - + -
148D LEU 5.6 0.4 - - - +
151D ASN* 4.0 20.9 - - - +
152D PHE* 3.8 39.7 - - + -
155D PHE* 4.1 20.4 - - + -
201D CL 4.0 16.6 - - + -
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Residues in contact with VAL 121 (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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27D PHE* 3.9 17.5 - - + -
56D TYR* 4.6 2.2 - - - +
108D VAL* 3.6 21.8 - - + -
109D ARG 3.5 11.0 - - - +
110D VAL* 4.3 7.9 - - + -
111D VAL* 4.7 0.9 - - - -
119D ALA* 4.4 1.3 - - + -
120D MET* 1.3 80.3 - - - +
122D PHE* 1.3 62.1 + - - +
123D PHE* 3.5 25.4 - - + -
135D VAL* 3.2 7.2 - - - +
136D THR* 2.9 40.5 + - - +
138D TYR* 3.6 30.7 - - + -
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Residues in contact with PHE 122 (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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11D PRO* 4.1 25.4 - - + -
13D LEU* 4.0 22.7 - - + -
16D VAL* 3.7 33.2 - - + -
107D LEU* 4.4 6.5 - - + -
108D VAL* 3.4 5.0 - - - -
109D ARG* 2.8 46.8 + - + +
111D VAL* 3.9 5.1 - - + +
121D VAL* 1.3 73.1 - - - +
123D PHE* 1.3 62.6 + - - +
124D LYS* 3.9 23.8 - - + -
133D PHE* 3.6 38.6 - + + -
134D TRP 3.5 3.1 - - - -
135D VAL* 4.1 19.7 - - + +
155D PHE* 5.5 0.2 - - + -
159D LEU* 4.3 3.6 - - + -
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Residues in contact with PHE 123 (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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52D TRP* 6.6 0.2 - + - -
54D THR* 6.1 0.4 - - + -
56D TYR* 3.9 2.2 - - - -
81D GLN* 5.5 1.8 - - - -
83D PHE* 3.9 20.0 - + - -
94D LEU* 6.1 0.9 - - + -
107D LEU 3.5 4.9 - - - +
108D VAL* 3.8 29.2 - - + -
121D VAL* 3.5 24.5 - - + -
122D PHE* 1.3 77.8 - - - +
124D LYS* 1.3 60.4 + - - +
133D PHE* 3.1 7.7 - - - +
134D TRP* 2.7 81.5 + + + +
136D THR* 3.4 29.8 - - + -
138D TYR* 3.5 21.1 - - - -
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Residues in contact with LYS 124 (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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10D ALA* 3.9 24.0 - - + -
11D PRO 5.9 0.4 - - - +
13D LEU* 5.2 9.9 - - + -
106D GLY* 3.0 3.3 - - - -
107D LEU* 2.9 60.1 + - + +
122D PHE* 3.9 13.9 - - + -
123D PHE* 1.3 76.2 - - - +
125D VAL* 1.3 75.0 + - - +
126D VAL* 4.8 8.8 - - - +
131D GLU* 2.7 31.3 + - + +
132D VAL 3.3 12.3 - - - +
133D PHE* 4.0 4.9 - - + -
134D TRP* 4.8 0.4 - - - -
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Residues in contact with VAL 125 (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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94D LEU* 4.2 14.4 - - + -
105D SER 3.1 11.7 - - - +
106D GLY* 4.0 0.2 - - - -
123D PHE* 6.1 0.2 - - + -
124D LYS* 1.3 83.2 - - - +
126D VAL* 1.3 62.3 + - - +
127D TRP* 4.3 3.1 - - + -
131D GLU* 3.5 4.7 - - - -
132D VAL* 2.9 39.4 + - + +
134D TRP* 3.8 19.3 - - + -
8S ILE* 3.7 24.2 - - + -
9S PHE 4.1 6.5 - - - +
10S CYS* 3.9 4.7 - - - -
13S CYS* 3.5 32.8 - - - -
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Residues in contact with VAL 126 (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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104D THR* 3.6 33.9 - - - +
105D SER* 2.8 30.2 + - - +
124D LYS* 4.8 10.5 - - - +
125D VAL* 1.3 76.7 - - - +
127D TRP* 1.3 60.7 + - - +
128D GLN 4.3 0.6 + - - +
129D ASN* 4.6 17.3 - - - +
130D ARG 3.4 9.0 - - - +
131D GLU* 4.6 15.7 - - + +
8S ILE* 4.7 0.2 - - - +
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Residues in contact with TRP 127 (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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104D THR* 4.7 8.1 - - + -
125D VAL* 3.8 2.7 + - + -
126D VAL* 1.3 73.4 - - - +
128D GLN* 1.3 101.3 + - + +
129D ASN 3.1 0.7 - - - -
130D ARG* 2.8 48.5 + - - +
132D VAL* 4.3 7.4 - - + -
78F TYR* 5.0 0.2 - - - -
6S ILE 4.9 1.3 - - - -
8S ILE* 4.0 19.7 - - + -
13S CYS* 3.5 51.2 + - + -
14S CYS* 4.0 13.1 - - + +
22S CYS* 3.5 37.7 - - + -
23S CYS 3.5 25.1 - - - -
24S LYS* 3.7 19.3 - - + -
25S THR 5.5 0.2 - - - -
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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