Contacts of the strand formed by residues 39 - 48 (chain A) in PDB entry 1H1B
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 GLY 39 (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* 3.3 2.1 - - - -
35A LEU* 2.9 36.9 + - - +
36A ARG 3.3 1.4 + - - -
38A GLY* 1.3 78.3 - - - +
40A HIS* 1.3 67.6 + - - -
41A PHE* 3.3 5.7 + - - +
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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* 2.8 24.3 + - - +
33A LEU 3.5 5.8 - - - -
34A GLN* 3.8 7.7 - - + +
38A GLY 3.8 3.4 + - - -
39A GLY* 1.3 71.4 - - - -
41A PHE* 1.3 60.7 + - - +
42A CYS 3.0 32.1 + - - -
43A GLY* 3.9 2.7 - - - -
73A LEU* 3.5 25.6 - - + +
141A TRP* 3.8 40.4 - + + +
151A ILE* 4.5 15.3 - - + +
192A PHE* 5.4 2.6 - - - -
193A GLY* 2.9 30.1 + - - -
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Residues in contact with PHE 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* 3.0 35.5 + - + -
34A GLN 3.6 23.3 - - - -
35A LEU* 3.7 26.0 - - + -
39A GLY 3.7 2.7 - - - +
40A HIS* 1.3 78.7 - - - +
42A CYS* 1.3 83.7 + - + +
58A CYS 3.5 25.4 - - - -
59A VAL* 5.1 2.5 - - + -
62A VAL* 4.7 13.7 - - + -
65A VAL* 4.1 22.9 - - + -
192A PHE* 4.5 22.0 - - + -
193A GLY* 4.2 10.3 + - - -
400A 151 5.4 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* 3.0 30.0 + - + +
40A HIS* 3.0 13.3 + - - -
41A PHE* 1.3 99.2 - - + +
43A GLY* 1.3 64.0 + - - +
58A CYS* 2.0 55.2 - - + -
193A GLY 3.9 6.3 - - - -
195A SER* 3.2 15.5 - - - +
400A 151 5.7 4.7 - - - -
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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 MET* 3.9 5.8 - - - -
31A VAL 3.2 13.2 - - - -
33A LEU* 3.8 3.7 - - - +
40A HIS* 3.9 4.1 - - - -
42A CYS* 1.3 75.3 - - - +
44A ALA* 1.3 63.1 + - - +
54A SER* 3.0 20.3 + - - -
193A GLY 4.1 1.0 + - - -
195A SER 2.8 10.7 + - - -
196A GLY* 3.2 10.0 - - - +
197A SER* 3.7 17.4 + - - -
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Residues in contact with ALA 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 PHE 3.8 0.5 - - - +
30A MET* 3.8 3.3 - - - +
31A VAL* 2.8 51.0 + - + -
33A LEU* 4.1 11.0 - - + -
43A GLY* 1.3 74.6 - - - +
45A THR* 1.3 63.7 + - - +
52A VAL* 4.1 9.4 - - + -
53A MET 3.4 10.8 - - - +
54A SER* 3.9 9.6 - - - -
196A GLY 3.4 12.4 + - - -
197A SER* 4.3 1.6 - - - +
198A PRO* 4.0 6.2 - - - +
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Residues in contact with THR 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 PHE* 3.5 13.7 - - + +
31A VAL* 4.0 0.2 - - - -
44A ALA* 1.3 73.2 - - - +
46A LEU* 1.3 73.5 + - - +
47A ILE* 3.2 11.2 + - + +
52A VAL* 3.1 5.5 - - - -
53A MET* 2.8 45.8 + - + +
121A ALA* 4.0 20.2 - - + -
196A GLY 4.9 0.3 + - - -
197A SER 4.8 0.5 - - - -
198A PRO* 3.1 32.9 - - - +
209A ILE* 4.3 11.3 - - + +
212A ILE* 5.8 2.0 - - - +
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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 5.2 0.2 - - - +
29A PHE* 3.1 17.6 + - - +
31A VAL* 3.6 9.1 - - + +
45A THR* 1.3 74.5 - - - +
47A ILE* 1.3 57.3 + - - +
48A ALA 2.9 27.6 - - - +
49A PRO* 4.4 6.5 - - + +
51A PHE 3.3 12.6 - - - +
52A VAL* 3.8 13.9 - - + -
68A LEU* 4.2 15.5 - - + -
108A LEU* 4.6 2.9 - - + -
112A ALA* 4.4 6.5 - - + -
114A ILE* 4.7 2.7 - - + -
118A VAL* 3.5 31.9 - - + -
119A GLN 4.0 19.5 - - - +
120A VAL* 3.6 7.8 - - + +
121A ALA 3.0 24.3 + - - -
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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 THR* 3.2 14.5 + - + +
46A LEU* 1.3 73.7 - - - +
48A ALA* 1.3 56.9 + - - +
51A PHE* 2.9 22.8 + - + +
52A VAL 4.2 2.7 - - - +
53A MET* 3.3 49.1 - - + -
105A ILE* 4.2 17.5 - - + -
120A VAL* 3.5 17.4 - - - +
121A ALA* 4.7 3.8 - - + +
123A LEU* 4.1 21.4 - - + +
238A ILE* 3.9 26.9 - - + -
242A ILE* 3.1 22.4 - - + +
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Residues in contact with ALA 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* 2.9 19.8 - - - +
47A ILE* 1.3 74.7 - - - +
49A PRO* 1.3 75.4 - - + +
50A ASN* 2.8 5.8 + - - +
51A PHE* 3.1 20.1 + - + -
120A VAL* 3.6 12.5 - - - +
242A ILE* 3.2 31.4 - - + -
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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