Contacts of the strand formed by residues 38 - 48 (chain A) in PDB entry 2ANW
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 GLN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLN* 3.2 26.1 + - + -
35A VAL 3.1 11.0 - - - -
36A LYS* 3.5 23.1 - - + -
38A ALA* 1.3 73.9 - - + -
39A ARG* 1.3 69.5 - - + +
65A ARG* 3.0 41.4 - - - -
67A TYR* 2.9 25.1 - + - -
76A ILE* 4.5 4.8 - - + -
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Residues in contact with ARG 39 (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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34A GLN* 3.1 6.1 - - - -
35A VAL* 2.8 42.6 + - + +
38A GLN* 1.3 112.5 - - + +
40A HIS* 1.6 60.1 - - - +
41A LEU* 3.5 7.1 + - + -
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Residues in contact with HIS 40 (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 SER* 2.9 22.4 + - - -
33A LEU 3.9 2.2 + - - -
34A GLN* 3.6 19.8 - - - +
39A ARG* 1.6 59.1 - - - +
41A LEU* 1.6 53.1 + - - +
42A CYS 3.0 32.3 + - - -
43A GLY* 4.0 1.1 - - - -
73A LEU* 3.6 25.2 - - + +
141A TRP* 3.9 25.2 - + + +
151A ILE* 3.8 38.8 - - + +
193A GLY 2.7 26.1 + - - -
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Residues in contact with LEU 41 (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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33A LEU 2.9 10.7 + - - +
35A VAL* 3.5 46.9 - - + -
39A ARG* 3.5 6.9 + - + +
40A HIS* 1.6 61.0 - - - +
42A CYS* 1.4 74.2 + - - +
58A CYS 4.4 3.6 - - - +
60A LEU* 3.6 20.2 - - + -
65A TRP* 3.6 10.1 - - + -
151A ILE* 6.1 0.2 - - - -
193A GLY* 3.6 17.7 + - - -
195A SER* 5.1 0.3 - - - -
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Residues in contact with CYS 42 (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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33A LEU* 2.9 36.8 + - + -
40A HIS* 3.0 15.0 + - - -
41A LEU* 1.4 90.9 - - + +
43A GLY* 1.3 64.9 + - - +
57A HIS* 5.2 0.9 - - - -
58A CYS* 2.0 55.0 - - + -
193A GLY 3.8 5.4 - - - -
195A SER* 3.0 20.4 - - - +
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Residues in contact with GLY 43 (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 GLN* 3.6 12.1 - - - -
31A VAL 3.4 12.3 - - - -
33A LEU* 3.6 7.8 - - - +
40A HIS* 4.4 3.4 - - - -
42A CYS* 1.3 77.0 - - - +
44A GLY* 1.3 57.8 + - - -
54A THR* 2.9 20.3 + - - -
140A GLY* 6.1 0.9 - - - -
193A GLY 3.9 6.4 + - - -
194A ASP* 4.2 2.0 + - - -
195A SER 2.8 10.6 + - - +
196A GLY 3.3 9.1 - - - -
197A GLY* 4.0 5.4 - - - -
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Residues in contact with GLY 44 (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 TRP 3.6 0.9 - - - +
30A GLN* 3.7 7.4 + - - -
31A VAL* 3.0 42.0 + - - -
33A LEU* 4.5 0.7 - - - -
43A GLY* 1.3 74.6 - - - -
45A SER* 1.3 62.3 + - - -
52A VAL* 4.2 4.7 - - - -
53A LEU 3.4 12.8 - - - -
54A THR* 4.2 1.6 - - - -
196A GLY 3.4 7.0 + - - -
197A GLY* 3.7 2.0 - - - -
198A PRO* 3.9 2.2 - - - +
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Residues in contact with SER 45 (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 TRP* 3.3 6.7 - - - -
44A GLY* 1.3 70.3 - - - -
46A LEU* 1.3 63.0 + - - +
47A ILE* 3.3 4.0 + - - +
52A VAL* 3.3 5.1 - - - +
53A LEU* 2.8 38.8 + - - -
121A ILE* 3.9 20.6 - - - -
196A GLY 5.0 0.3 + - - -
197A GLY 4.3 1.2 - - - -
198A PRO* 3.3 36.9 - - - +
209A LEU* 3.9 15.2 - - - +
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Residues in contact with LEU 46 (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 PRO 4.8 1.6 - - - +
29A TRP* 2.9 22.2 + - - +
31A VAL* 4.2 10.5 - - + +
44A GLY 4.2 0.4 - - - -
45A SER* 1.3 70.3 - - - +
47A ILE* 1.3 59.0 + - - +
48A GLY 3.1 26.5 - - - +
49A HIS 4.6 0.7 - - - +
51A TRP 3.5 9.9 - - - +
52A VAL* 4.1 13.5 - - + -
68A SER* 5.5 1.1 - - - -
108A LEU* 4.6 4.5 - - + -
112A LEU* 4.1 24.2 - - + -
114A TYR* 4.3 13.7 - - + -
118A GLN* 4.4 15.3 - - + -
119A LYS 3.9 28.5 - - - +
120A PRO* 3.1 4.0 - - + +
121A ILE* 3.0 27.4 + - - +
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Residues in contact with ILE 47 (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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45A SER 3.3 9.6 + - - +
46A LEU* 1.3 77.9 - - - +
48A GLY* 1.3 56.4 + - - +
51A TRP* 3.0 32.5 + - + +
52A VAL 4.3 0.7 - - - +
53A LEU* 4.2 15.9 - - + +
105A LEU* 3.6 30.7 - - + -
120A PRO* 3.5 13.6 - - - +
121A ILE* 4.1 19.5 - - + +
123A LEU* 3.9 34.4 - - + +
209A LEU* 4.4 2.0 - - + -
238A ILE* 4.4 15.9 - - + -
242A THR* 4.7 4.0 - - + -
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Residues in contact with GLY 48 (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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46A LEU* 3.1 21.0 - - - +
47A ILE* 1.3 76.4 - - - +
49A HIS* 1.3 66.0 + - - -
50A GLN 3.1 4.4 + - - -
51A TRP* 3.4 13.0 + - - +
114A TYR* 3.0 17.7 - - - -
120A PRO* 3.8 1.6 - - - +
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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