Contacts of the strand formed by residues 39 - 48 (chain A) in PDB entry 2D9F
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 VAL 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN* 1.3 70.5 - - - +
40A VAL* 1.3 59.2 + - - +
41A THR* 4.1 8.4 + - - +
61A VAL* 3.3 30.5 - - + -
62A PHE 3.6 6.1 - - - +
63A THR* 4.9 8.3 - - - +
120A THR 4.2 0.5 - - - +
121A ALA* 3.5 1.7 - - - -
122A VAL* 2.6 46.1 + - + +
123A ASP* 3.6 18.7 - - - +
124A ARG 3.6 20.0 - - - +
125A PRO* 4.2 11.4 - - + -
126A ASP* 4.6 3.6 - - + +
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Residues in contact with VAL 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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34A PRO* 4.1 16.4 - - + -
35A VAL 5.1 1.8 - - - +
38A GLN* 3.9 3.8 - - + +
39A VAL* 1.3 74.5 - - - +
41A THR* 1.3 61.1 + - - +
42A VAL* 4.0 1.9 + - + -
60A LEU 3.5 1.6 - - - +
61A VAL* 3.5 3.3 - - - -
62A PHE* 2.9 73.5 + - + +
64A LEU* 3.9 13.5 - - + -
77A VAL* 4.1 14.1 - - + -
118A LEU* 4.4 8.1 - - + -
120A THR 4.0 1.6 - - - -
121A ALA* 3.6 24.7 - - + -
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.3 7.1 + - - +
40A VAL* 1.3 73.6 + - - +
42A VAL* 1.3 63.5 + - - +
59A GLU* 3.9 31.2 - - + +
60A LEU 3.2 14.4 - - - +
61A VAL* 4.2 13.4 - - + +
118A LEU* 4.5 0.4 - - - +
119A LYS* 3.3 31.4 + - + +
120A THR* 3.1 26.5 + - - +
122A VAL* 6.0 0.9 - - - +
126A ASP* 4.2 15.5 + - - +
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Residues in contact with VAL 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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40A VAL* 4.0 4.2 + - + +
41A THR* 1.3 82.2 - - - +
43A HIS* 1.3 67.2 + - - +
44A LEU 4.3 1.3 - - - +
58A PRO 3.5 4.5 - - - +
59A GLU* 4.1 0.5 - - - -
60A LEU* 2.9 53.0 + - + +
62A PHE* 5.0 0.2 - - + -
73A LEU* 3.8 21.5 - - + -
77A VAL* 4.2 12.6 - - + -
116A VAL* 3.9 7.2 - - + -
117A THR 3.0 18.2 - - - +
118A LEU* 3.3 32.8 - - + -
119A LYS* 4.1 3.8 - - - -
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Residues in contact with HIS 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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42A VAL* 1.3 79.7 - - - +
44A LEU* 1.3 52.7 + - - +
45A GLN* 3.2 39.0 + - + +
56A GLU* 4.1 8.0 - - + +
57A GLU 3.0 24.8 + - - -
58A PRO* 3.6 27.4 + - + +
115A GLU* 2.4 28.6 - - - +
117A THR* 3.3 25.5 + - + +
119A LYS* 5.0 9.4 - - + -
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Residues in contact with LEU 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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42A VAL* 4.0 6.8 + - + +
43A HIS* 1.3 73.0 - - - +
45A GLN* 1.3 87.3 + - - +
46A THR* 3.8 13.0 - - - +
55A GLN* 4.2 14.4 - - - +
57A GLU* 3.1 44.0 + - + +
60A LEU* 4.5 9.5 - - + +
70A ILE* 5.4 8.3 - - + -
73A LEU* 4.6 27.8 - - + -
114A LEU* 3.6 33.2 - - + -
115A GLU 3.5 5.4 - - - +
116A VAL* 5.5 1.6 - - + -
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Residues in contact with GLN 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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43A HIS* 3.2 37.6 + - + +
44A LEU* 1.3 80.8 - - - +
46A THR* 1.3 61.7 + - - +
47A SER* 4.0 2.8 + - - +
53A ARG* 3.3 28.5 - - - +
55A GLN 4.0 4.5 - - - +
56A GLU* 3.0 34.1 + - + +
113A CYS 2.9 16.8 - - - +
114A LEU* 3.4 7.6 - - - -
115A GLU* 3.7 19.5 + - + +
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Residues in contact with THR 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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44A LEU* 3.8 6.3 - - - +
45A GLN* 1.3 73.4 - - - +
47A SER* 1.3 64.0 + - - +
53A ARG* 3.4 4.5 - - - +
54A VAL* 3.0 32.7 + - + -
55A GLN* 3.3 45.9 + - - +
70A ILE* 5.9 1.9 - - - +
96A TYR* 3.9 12.5 + - + +
112A LEU* 3.9 27.1 - - + -
114A LEU* 3.4 25.5 - - + +
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Residues in contact with SER 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 GLN* 4.0 2.3 + - - +
46A THR* 1.3 78.9 - - - +
48A LEU* 1.3 68.7 + - - +
51A GLY* 5.0 3.8 - - - -
52A THR 3.8 8.3 - - - -
53A ARG* 4.0 22.0 - - - -
54A VAL 4.2 0.2 - - - +
112A LEU* 3.4 5.6 - - - -
113A CYS* 2.8 56.5 + - - +
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Residues in contact with LEU 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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47A SER* 1.3 77.2 - - - +
49A GLU* 1.3 67.9 + - + +
50A ASN* 2.7 29.3 + - - +
51A GLY* 2.7 15.4 + - - -
52A THR* 3.2 22.3 + - + +
54A VAL* 3.0 37.2 - - + -
107A PRO* 4.4 24.9 - - + -
110A ALA* 4.6 5.4 - - + -
111A ALA 4.3 4.0 - - - +
112A LEU* 3.6 20.4 - - + -
113A CYS* 5.3 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