Contacts of the strand formed by residues 38 - 45 (chain B) in PDB entry 2D4H
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 MET 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.2 9.9 - - + -
34B ILE* 3.6 42.0 - - + -
36B GLN 3.5 14.1 - - - +
37B PRO* 1.3 75.0 - - - +
39B VAL* 1.3 59.3 + - - +
40B VAL* 3.6 6.7 - - + -
92B ILE* 3.2 13.9 - - + +
94B VAL* 3.7 31.4 - - + -
279B THR* 3.2 6.8 - - - +
280B LYS* 2.9 30.3 + - - +
288B VAL* 3.1 13.2 + - + +
289B ASN 3.4 24.5 - - - +
290B GLY* 3.8 8.5 - - - -
293B LEU* 4.3 12.8 - - - -
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PRO 4.3 0.2 + - - -
38B MET* 1.3 71.9 - - - +
40B VAL* 1.3 60.2 + - - +
41B VAL* 4.2 3.6 - - + -
85B HIS* 3.8 27.6 - - + +
88B LYS* 4.2 5.6 - - + -
91B HIS* 4.1 17.0 - - + -
92B ILE 2.8 9.4 + - - +
93B LEU* 3.5 17.5 - - + +
94B VAL 3.1 20.9 + - - +
124B SER* 4.0 2.5 - - - +
277B SER* 3.4 31.6 - - - +
278B LYS 3.3 25.6 - - - +
279B THR* 4.0 7.9 - - - -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MET* 3.6 10.7 + - + +
39B VAL* 1.3 72.2 - - - +
41B VAL* 1.3 63.2 + - - +
94B VAL* 3.5 22.2 - - + +
96B LEU* 3.6 30.1 - - + -
122B LEU 3.4 27.1 - - - +
123B SER* 3.8 5.8 - - - -
124B SER* 2.8 38.1 + - - +
125B THR 3.1 4.7 + - - -
280B LYS* 3.8 17.9 - - + -
288B VAL* 5.1 0.2 - - + -
293B LEU* 3.8 18.4 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 4.0 8.5 - - + +
40B VAL* 1.3 79.6 - - - +
42B ALA* 1.3 55.2 - - - +
43B ILE* 4.0 21.2 + - + +
58B LEU* 4.7 1.8 - - + -
93B LEU* 3.8 26.9 - - + -
94B VAL 2.8 12.2 + - - +
95B LEU* 3.4 14.4 - - + +
96B LEU* 2.8 33.9 + - - +
123B SER* 4.6 0.7 - - - -
125B THR* 3.8 18.4 - - - -
127B VAL* 4.4 10.8 - - + -
273B ILE* 3.8 27.4 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 1.3 73.1 - - - +
43B ILE* 1.3 63.9 + - - +
44B VAL* 3.8 11.7 - - + +
96B LEU* 3.5 11.2 - - + -
119B ALA* 3.4 34.8 - - + +
123B SER* 3.7 10.7 - - - +
125B THR 3.2 9.3 + - - +
126B PHE* 4.8 3.6 - - + -
127B VAL* 2.9 33.8 + - - +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 4.2 8.5 - - + +
42B ALA* 1.3 73.0 - - - +
44B VAL* 1.3 61.8 + - - +
51B LYS* 3.8 36.6 - - + +
54B LEU* 4.3 15.5 - - + -
55B MET* 4.7 16.2 - - + -
58B LEU* 4.1 26.7 - - + -
95B LEU* 5.3 2.5 - - + -
96B LEU 2.6 15.7 + - - +
97B ASP* 3.3 11.6 - - + +
98B THR* 3.2 22.9 + - - -
127B VAL* 3.8 33.4 - - + -
129B ASN* 4.9 2.9 - - + -
269B PHE* 4.6 4.3 - - + -
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 4.1 6.5 - - + +
43B ILE* 1.3 78.7 - - - +
45B GLY* 1.3 56.0 + - - +
51B LYS* 3.7 4.7 - - - -
98B THR* 3.0 26.7 - - + +
116B PHE* 3.4 41.7 - - + -
119B ALA* 4.0 16.4 - - + -
126B PHE* 3.7 23.8 - - + -
127B VAL 3.1 6.5 + - - +
128B TYR* 3.7 10.7 - - + -
129B ASN* 2.8 34.1 + - - +
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 1.3 81.0 - - - +
46B LEU* 1.3 64.5 + - - -
49B THR* 4.5 0.2 - - - -
51B LYS* 3.0 20.8 + - - +
98B THR* 3.1 6.8 + - - +
101B LEU* 3.3 23.3 - - - +
128B TYR* 4.6 7.9 - - - -
129B ASN 3.4 14.8 - - - -
141B GLN* 6.0 0.4 - - - -
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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