Contacts of the strand formed by residues 85 - 97 (chain A) in PDB entry 5ES4
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 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.7 5.6 - - - -
79A SER* 3.3 9.5 + - - -
80A THR* 3.1 44.2 + - + +
83A PRO* 3.5 18.2 + - + +
84A SER* 1.3 83.8 - - - +
86A LEU* 1.3 60.3 + - - +
109A LEU* 4.5 13.6 - - + +
110A LEU 3.4 5.6 - - - +
114A GLN* 3.3 34.6 + - - +
341A PHE* 3.2 27.5 - - + -
346A PRO* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.8 21.5 - - + -
25A TYR* 3.7 20.5 - - + -
31A VAL* 3.5 35.2 - - + -
47A LEU* 4.8 7.4 - - + -
60A ILE* 4.6 12.3 - - + -
77A LEU* 3.9 13.7 - - + -
78A ALA 3.1 19.7 - - - +
79A SER* 4.4 3.1 - - - -
85A GLN* 1.3 73.1 - - - +
87A LEU* 1.3 65.9 + - - +
88A ALA 4.1 1.6 - - - +
108A PHE 3.8 0.3 - - - +
109A LEU* 3.4 5.1 - - - +
110A LEU* 2.7 55.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER 4.2 0.2 - - - +
77A LEU* 3.6 5.4 - - - +
78A ALA* 3.0 31.2 + - + +
86A LEU* 1.3 75.4 - - - +
88A ALA* 1.3 58.4 + - - +
89A CYS* 3.6 16.8 - - - -
107A CYS* 4.3 3.4 - - + -
108A PHE 3.2 9.4 - - - +
109A LEU* 3.9 18.6 - - + -
119A LEU* 4.9 5.8 - - + -
339A ALA* 3.4 32.5 - - + -
340A VAL 5.5 0.9 - - - +
341A PHE* 3.6 21.8 - - + -
346A PRO* 3.6 31.9 - - + -
347A VAL 5.7 0.2 - - - +
348A LEU* 3.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.4 35.2 - - + -
73A LEU* 5.7 2.9 - - + -
74A GLY 5.4 1.1 - - - +
76A SER 3.9 4.3 - - - -
77A LEU* 4.0 8.7 - - + -
86A LEU* 4.1 2.6 - - + -
87A LEU* 1.3 72.5 - - - +
89A CYS* 1.3 65.0 + - - +
107A CYS* 3.0 3.8 - - - -
108A PHE* 2.6 52.1 + - + +
110A LEU* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 4.8 0.7 - - - -
73A LEU* 3.3 6.0 - - - -
74A GLY 3.0 20.3 + - - +
75A LEU 3.5 0.3 + - - -
76A SER* 3.1 29.5 + - - +
87A LEU* 3.6 17.5 - - - -
88A ALA* 1.3 76.8 - - - +
90A GLY* 1.3 60.6 + - - +
91A PRO* 4.0 1.6 - - + -
106A LEU 3.7 5.2 - - - +
107A CYS* 2.0 47.6 - - - -
335A GLU 5.6 0.2 - - - +
336A GLY 3.4 21.3 - - - +
339A ALA* 4.4 4.5 - - - -
348A LEU* 4.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 3.0 44.3 - - - +
72A SER 3.5 8.5 - - - -
73A LEU* 3.5 7.0 - - - -
89A CYS* 1.3 72.6 - - - +
91A PRO* 1.3 62.9 - - - +
92A THR 3.3 1.6 + - - -
93A VAL* 3.3 10.6 - - - +
106A LEU 3.2 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET 4.1 1.3 - - - +
75A LEU* 4.0 25.8 - - + -
76A SER* 4.9 1.3 - - - -
89A CYS* 4.0 7.4 - - + +
90A GLY* 1.3 85.7 - - - +
92A THR* 1.3 59.2 + - + +
93A VAL 3.4 2.9 - - - -
104A THR 3.8 3.1 - - - +
105A GLY* 4.0 9.6 - - - -
106A LEU 4.7 0.2 - - - +
334A GLN* 3.0 54.4 - - + +
335A GLU 4.0 1.3 - - - +
336A GLY 4.0 5.2 - - - +
337A PHE* 3.7 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN 2.7 25.9 + - - +
71A MET* 2.4 33.5 + - - +
72A SER* 3.4 10.6 + - - -
75A LEU* 5.0 10.5 - - + -
91A PRO* 1.3 88.5 - - + +
93A VAL* 1.3 60.0 + - - +
94A HIS* 3.1 9.8 + - - -
103A LEU* 3.3 22.4 - - + +
334A GLN* 3.8 15.0 - - - +
337A PHE* 6.2 1.1 - - + -
156B PRO* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU 4.6 1.8 - - - +
68A ALA* 3.5 31.9 - - + -
69A VAL 3.5 4.5 - - - -
71A MET* 3.4 14.1 - - + +
90A GLY 3.3 19.5 - - - +
92A THR* 1.3 73.0 - - - +
94A HIS* 1.3 67.7 + - - +
95A HIS* 5.2 2.5 - - + +
102A TYR 3.0 12.8 - - - +
103A LEU* 3.0 11.4 - - - -
104A THR* 2.9 39.6 + - + +
105A GLY 4.1 0.4 - - - -
106A LEU* 3.6 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU 4.4 1.2 - - - +
69A VAL* 2.6 36.5 + - + +
70A ASN* 3.4 34.4 + - + +
92A THR* 3.1 23.2 + - - -
93A VAL* 1.3 80.3 - - - +
95A HIS* 1.3 61.4 + - - +
96A GLU 4.3 0.2 - - - -
101A MET* 4.2 17.5 - - + -
102A TYR 3.2 4.3 - - - -
103A LEU* 3.5 7.5 - - + +
155B LEU* 3.4 37.4 + - + +
160B THR* 5.0 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.0 42.0 + - + +
93A VAL* 4.3 3.7 - - - +
94A HIS* 1.3 75.0 + - - +
96A GLU* 1.3 63.2 + - - +
97A CYS* 3.7 21.6 + - - -
101A MET* 3.2 7.8 - - - -
102A TYR* 2.7 51.2 + + + +
104A THR* 4.8 15.9 - - + +
124A GLN* 2.7 37.0 + - + -
125A GLU* 4.7 0.4 - - - -
126A CYS* 4.0 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A HIS* 1.3 74.1 + - - +
97A CYS* 1.3 60.4 + - - +
98A GLY* 3.1 25.8 + - - +
100A ASN 3.4 4.3 - - - -
101A MET* 3.9 15.2 - - + +
126A CYS* 3.9 7.3 - - - -
161B HIS* 2.5 34.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A HIS* 3.7 6.9 + - - -
96A GLU* 1.3 71.0 - - - +
98A GLY* 1.3 58.0 + - - +
99A ARG* 3.0 8.8 + - - +
100A ASN* 2.7 16.3 + - + +
102A TYR* 3.7 27.8 - - + +
126A CYS* 2.0 53.2 - - + -
127A PRO* 3.5 17.0 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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